OBO Relations Ontology
type: Ontology
version IRI: ro-base.owl
type: IAO_8000001
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
license: https://creativecommons.org/publicdomain/zero/1.0/
version info: 2025-06-24

temporal interpretation
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

never in taxon
type: AnnotationProperty
IAO_0000112: tooth SubClassOf 'never in taxon' value 'Aves'
IAO_0000115: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
IAO_0000425: Class: ?X DisjointWith: RO_0002162 some ?Y
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }
sub property of: taxonomic class assertion

mutually spatially disjoint with
type: AnnotationProperty
IAO_0000115: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
IAO_0000118: non-overlapping with
IAO_0000118: shares no parts with
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
OMO_0002000: PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . }
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
IAO_0000115: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
sub property of: logical macro assertion on a class

ambiguous for taxon
type: AnnotationProperty
IAO_0000115: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
sub property of: taxonomic class assertion

dubious for taxon
type: AnnotationProperty
IAO_0000115: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
comment: This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
sub property of: taxonomic class assertion

present in taxon
type: AnnotationProperty
IAO_0000115: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
sub property of: taxonomic class assertion

defined by inverse
type: AnnotationProperty
sub property of: SubsetProperty

logical macro assertion
type: AnnotationProperty
IAO_0000115: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

annotation property cardinality
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
sub property of: logical macro assertion on an annotation property

logical macro assertion on a class
type: AnnotationProperty
IAO_0000115: A logical macro assertion whose domain is an IRI for a class
IAO_0000116: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
sub property of: logical macro assertion

logical macro assertion on a property
type: AnnotationProperty
IAO_0000115: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
IAO_0000115: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty
sub property of: logical macro assertion on a property

dispositional interpretation
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
sub property of: logical macro assertion on an object property

has no connections with
type: AnnotationProperty
IAO_0000112: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
IAO_0000115: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
IAO_0000118: shares no connection with
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
IAO_0000115: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
sub property of: inherited annotation property

always present in taxon
type: AnnotationProperty
IAO_0000112: brain always_present_in_taxon 'Vertebrata'
IAO_0000112: forelimb always_present_in_taxon Euarchontoglires
IAO_0000115: S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
IAO_0000116: This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
IAO_0000118: never lost in
sub property of: present in taxon

temporal logical macro assertion on a class
type: AnnotationProperty
IAO_0000232: This property was originally created for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
sub property of: logical macro assertion on a class

measurement property has unit
type: AnnotationProperty
sub property of: logical macro assertion on an annotation property

has start time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

has end time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

start, days post fertilization
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
sub property of: has start time value

end, days post fertilization
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
sub property of: has end time value

start, years post birth
type: AnnotationProperty
IAO_0000115: Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
sub property of: has start time value

end, years post birth
type: AnnotationProperty
IAO_0000115: Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
sub property of: has end time value

start, months post birth
type: AnnotationProperty
IAO_0000115: Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
sub property of: has start time value

end, months post birth
type: AnnotationProperty
IAO_0000115: Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
sub property of: has end time value

month of gestation
type: AnnotationProperty
IAO_0000115: Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
sub property of: temporal logical macro assertion on a class

has developmental stage marker
type: AnnotationProperty
IAO_0000115: A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
sub property of: temporal logical macro assertion on a class

start, days post coitum
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the start of the stage and the time of coitum.
IAO_0000232: For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
sub property of: has start time value

end, days post coitum
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the end of the stage and the time of coitum.
sub property of: has end time value

start, weeks post birth
type: AnnotationProperty
sub property of: has start time value

end, weeks post birth
type: AnnotationProperty
sub property of: has end time value

is asymmetric relational form of process class
type: AnnotationProperty
IAO_0000115: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
sub property of: is relational form of process class

is symmetric relational form of process class
type: AnnotationProperty
IAO_0000115: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
sub property of: is relational form of process class

is relational form of process class
type: AnnotationProperty
IAO_0000115: R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
sub property of: is relational form of a class

is direct form of
type: AnnotationProperty
IAO_0000115: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
IAO_0000116: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: https://orcid.org/0000-0002-6601-2165
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
IAO_0000115: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: https://orcid.org/0000-0002-6601-2165
sub property of: logical macro assertion on an object property

logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion

is a defining property chain axiom
type: AnnotationProperty
IAO_0000115: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
sub property of: logical macro assertion on an axiom

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
IAO_0000115: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
sub property of: is a defining property chain axiom

is relational form of a class
type: AnnotationProperty
IAO_0000115: An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
sub property of: logical macro assertion on an object property

logical macro assertion involving identity
type: AnnotationProperty
IAO_0000115: A shortcut relationship that holds between two entities based on their identity criteria
sub property of: logical macro assertion

in approximate one to one relationship with
type: AnnotationProperty
IAO_0000115: A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
sub property of: logical macro assertion involving identity

is approximately equivalent to
type: AnnotationProperty
IAO_0000115: x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
IAO_0000232: The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
sub property of: in approximate one to one relationship with

is opposite of
type: AnnotationProperty
IAO_0000112: 'anterior end of organism' is-opposite-of 'posterior end of organism'
IAO_0000112: 'increase in temperature' is-opposite-of 'decrease in temperature'
IAO_0000115: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: in approximate one to one relationship with

is indistinguishable from
type: AnnotationProperty
IAO_0000115: x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: is approximately equivalent to

evidential logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion on an axiom

axiom has evidence
type: AnnotationProperty
IAO_0000115: A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
IAO_0000232: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

axiom contradicted by evidence
type: AnnotationProperty
IAO_0000115: A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
IAO_0000232: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

is representative IRI for equivalence set
type: AnnotationProperty
IAO_0000112: In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
IAO_0000115: this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
IAO_0000232: If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
see also: OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
sub property of: logical macro assertion involving identity

nominally disjoint with
type: AnnotationProperty
IAO_0000115: true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.
creator: https://orcid.org/0000-0002-6601-2165
sub property of: logical macro assertion on an object property

is directional form of
type: AnnotationProperty
IAO_0000115: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

is homeomorphic for
type: AnnotationProperty
IAO_0000112: part-of is homeomorphic for independent continuants.
IAO_0000115: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-10-21T19:46:34Z
comment: R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
sub property of: logical macro assertion on an object property

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
IAO_0000115: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
temporal interpretation: axiom holds for all times
is homeomorphic for: BFO_0000002
is homeomorphic for: BFO_0000003
is homeomorphic for: BFO_0000004
is homeomorphic for: BFO_0000017
is homeomorphic for: BFO_0000019
is homeomorphic for: BFO_0000020
is homeomorphic for: BFO_0000031
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
IAO_0000115: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
temporal interpretation: axiom holds for all times
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: BFO_0000017
range: BFO_0000015
IAO_0000111: realized in
IAO_0000112: this disease is realized in this disease course
IAO_0000112: this fragility is realized in this shattering
IAO_0000112: this investigator role is realized in this investigation
IAO_0000118: is realized by
IAO_0000118: realized_in
IAO_0000600: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000017
IAO_0000111: realizes
IAO_0000112: this disease course realizes this disease
IAO_0000112: this investigation realizes this investigator role
IAO_0000112: this shattering realizes this fragility
IAO_0000115: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
IAO_0000600: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

obsolete preceded by
type: ObjectProperty
comment: accidentally included in BFO 1.2 proposal - should have been BFO_0000062
deprecated: true

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
IAO_0000111: preceded by
IAO_0000115: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part of
property chain axiom: happens during
IAO_0000111: precedes
IAO_0000115: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: BFO_0000003
range: BFO_0000004
property chain axiom: part of
IAO_0000111: occurs in
IAO_0000115: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
IAO_0000118: occurs_in
IAO_0000118: unfolds in
IAO_0000118: unfolds_in
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
IAO_0000111: site of
IAO_0000115: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
IAO_0000115: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
IAO_0000118: inheres_in
temporal interpretation: axiom holds for all times
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: BFO_0000020
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
IAO_0000115: Inverse of characteristic_of
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
inverse of: has participant
domain: BFO_0000002
range: BFO_0000003
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
IAO_0000115: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000002
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
IAO_0000115: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: BFO_0000031
range: Class
  union of: BFO_0000015
  union of: BFO_0000020
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
IAO_0000115: A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.

concretizes
type: ObjectProperty
domain: Class
  union of: BFO_0000015
  union of: BFO_0000020
range: BFO_0000031
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
IAO_0000115: A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: BFO_0000034
IAO_0000112: this catalysis function is a function of this enzyme
IAO_0000115: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
IAO_0000116: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
IAO_0000118: function_of
IAO_0000118: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000112: this red color is a quality of this apple
IAO_0000115: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
IAO_0000115: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
IAO_0000118: is role of
IAO_0000118: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: BFO_0000004
range: BFO_0000034
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
IAO_0000115: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
IAO_0000118: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: BFO_0000019
IAO_0000112: this apple has quality this red color
IAO_0000115: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
IAO_0000118: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: BFO_0000004
range: BFO_0000023
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
IAO_0000115: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
IAO_0000118: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: BFO_0000004
range: BFO_0000016
IAO_0000115: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
IAO_0000115: inverse of has disposition
in subset: defined by inverse
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

obsolete in neural circuit with
type: ObjectProperty
IAO_0000114: IAO_0000125
IAO_0000115: OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
deprecated: true

obsolete upstream in neural circuit with
type: ObjectProperty
IAO_0000114: IAO_0000125
IAO_0000115: OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
deprecated: true

obsolete downstream in neural circuit with
type: ObjectProperty
IAO_0000114: IAO_0000125
IAO_0000115: OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
deprecated: true

derives from
type: ObjectProperty
inverse of: derives into
IAO_0000112: this cell derives from this parent cell (cell division)
IAO_0000112: this nucleus derives from this parent nucleus (nuclear division)
IAO_0000114: IAO_0000125
IAO_0000115: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
IAO_0000118: derives_from
IAO_0000232: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
in subset: ro-eco

derives into
type: ObjectProperty
IAO_0000112: this parent cell derives into this cell (cell division)
IAO_0000112: this parent nucleus derives into this nucleus (nuclear division)
IAO_0000114: IAO_0000125
IAO_0000115: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
IAO_0000118: derives_into
in subset: ro-eco

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
IAO_0000111: is location of
IAO_0000112: my head is the location of my brain
IAO_0000112: this cage is the location of this rat
IAO_0000115: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
IAO_0000116: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000118: location_of
temporal interpretation: axiom holds for all times

obsolete contained in
type: ObjectProperty
IAO_0000111: contained in
IAO_0000116: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
IAO_0000116: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
IAO_0000118: contained_in
deprecated: true

obsolete contains
type: ObjectProperty
IAO_0000111: contains
deprecated: true

is allergic trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has allergic trigger
domain: BFO_0000040
IAO_0000112: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
IAO_0000115: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

is autoimmune trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has autoimmune trigger
domain: BFO_0000040
IAO_0000115: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has allergic trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: BFO_0000040
IAO_0000112: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
IAO_0000115: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has autoimmune trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: BFO_0000040
IAO_0000115: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

located in
type: ObjectProperty
type: TransitiveProperty
domain: BFO_0000004
domain: Class
  intersection of: BFO_0000004
  intersection of: Class
    complement of: BFO_0000006
range: BFO_0000004
range: Class
  intersection of: BFO_0000004
  intersection of: Class
    complement of: BFO_0000006
property chain axiom: part of
IAO_0000111: located in
IAO_0000112: my brain is located in my head
IAO_0000112: this rat is located in this cage
IAO_0000115: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
IAO_0000116: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
IAO_0000116: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000118: located_in
temporal interpretation: axiom holds for all times
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
in subset: valid for go gp2term

Axiom
annotated source: located in
annotated property: domain
annotated target: BFO_0000004
IAO_0000116: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: BFO_0000004
IAO_0000116: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
sub property of: mereotopologically related to
inverse of: has 2D boundary
IAO_0000112: the surface of my skin is a 2D boundary of my body
IAO_0000115: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
IAO_0000116: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
IAO_0000116: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
IAO_0000118: 2D_boundary_of
IAO_0000118: boundary of
IAO_0000118: is 2D boundary of
IAO_0000118: is boundary of
IAO_0000118: surface of
temporal interpretation: axiom holds for all times

aligned with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000116: May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000141
IAO_0000112: my body has 2D boundary the surface of my skin
IAO_0000115: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
IAO_0000116: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
IAO_0000116: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has boundary
IAO_0000118: has_2D_boundary
temporal interpretation: axiom holds for all times

electrically_synapsed_to
type: ObjectProperty
sub property of: connected to
IAO_0000115: A relation that holds between two neurons that are electrically coupled via gap junctions.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

tracheates
type: ObjectProperty
sub property of: located in
domain: UBERON_0000061
range: UBERON_0000061
IAO_0000115: The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
IAO_0000117: https://orcid.org/0000-0002-7073-9172

innervated by
type: ObjectProperty
inverse of: innervates
domain: UBERON_0000061
range: UBERON_0000122
property chain axiom: branching part of
IAO_0000115: relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

bounding layer of
type: ObjectProperty
sub property of: part of
domain: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002124
range: BFO_0000040
IAO_0000115: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
domain: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001199
range: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001199
IAO_0000115: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

cell expresses
type: ObjectProperty
sub property of: expresses
domain: CL_0000000
IAO_0000115: A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
description: x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y

regulates in another organism
type: ObjectProperty
sub property of: causally upstream of or within
domain: BFO_0000015
range: BFO_0000015
IAO_0000115: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
IAO_0000117: https://orcid.org/0000-0002-7073-9172
has exact synonym: regulates in other organism
in subset: valid for go ontology

regulates transport of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: transports or maintains localization of
IAO_0000115: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco

occurrent part of
type: ObjectProperty
sub property of: part of
sub property of: causally upstream of or within
domain: BFO_0000003
range: BFO_0000003
IAO_0000115: A part of relation that applies only between occurrents.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
IAO_0000115: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
IAO_0000115: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
IAO_0000115: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has necessary component activity
type: ObjectProperty
sub property of: has component activity
sub property of: positively regulated by
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:36:08Z
comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.

has component activity
type: ObjectProperty
sub property of: has component process
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: BFO_0000015
range: BFO_0000015
IAO_0000115: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:49:21Z

has ligand
type: ObjectProperty
sub property of: has input
IAO_0000115: A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-19T17:30:36Z

transports
type: ObjectProperty
sub property of: transports or maintains localization of
IAO_0000115: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-20T17:11:08Z

occurs across
type: ObjectProperty
sub property of: has part that occurs in
IAO_0000115: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-20T17:19:37Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
has db xref: https://orcid.org/0000-0002-7073-9172

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
IAO_0000115: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: IAO_0000115
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
has db xref: https://orcid.org/0000-0002-7073-9172

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
IAO_0000115: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: IAO_0000115
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
has db xref: https://orcid.org/0000-0002-7073-9172

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
IAO_0000115: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: IAO_0000115
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
has db xref: https://orcid.org/0000-0002-7073-9172

in register with
type: ObjectProperty
sub property of: mereotopologically related to
domain: image
range: image
IAO_0000115: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-12-07T12:58:06Z

Axiom
annotated source: in register with
annotated property: IAO_0000115
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
has db xref: https://orcid.org/0000-0002-7073-9172

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: <=
in subset: ro-eco
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: SymmetricProperty
type: TransitiveProperty
IAO_0000115: x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

starts before
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: starts during
property chain axiom: obsolete preceded by
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: ends_at_start_of
IAO_0000118: meets
is direct form of: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: BFO_0000003
range: BFO_0000003
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: io
in subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: d
IAO_0000118: during
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: o
IAO_0000118: overlaps
in subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

has soma location
type: ObjectProperty
sub property of: overlaps
domain: CL_0000540
range: UBERON_0000465
property chain axiom: part of
property chain axiom: is neuron
property chain axiom: is anatomical entity
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and a material anatomical entity that its soma is part of.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
temporal interpretation: axiom holds for all times

fasciculates with
type: ObjectProperty
sub property of: overlaps
inverse of: has fasciculating neuron projection
domain: CL_0000540
range: UBERON_0000122
IAO_0000114: IAO_0000125
IAO_0000115: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: fasciculates with
IAO_0000426: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

axon synapses in
type: ObjectProperty
sub property of: has presynaptic terminal in
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure its axon forms (chemical) synapses in.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed by
type: ObjectProperty
sub property of: receives input from
inverse of: synapsed to
range: Class
  union of: CL_0000540
  union of: Restriction
    on property: part of
    some values from: CL_0000540
IAO_0000114: IAO_0000125
IAO_0000115: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has plasma membrane part
type: ObjectProperty
sub property of: has part
domain: UBERON_0000465
range: UBERON_0000465
IAO_0000112: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
IAO_0000114: IAO_0000125
IAO_0000115: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
IAO_0000117: https://orcid.org/0000-0001-9990-8331
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-1617-8244
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19243617
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
temporal interpretation: axiom holds for all times

synapsed_via_type_Ib_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_Ib_bouton
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_via_type_Is_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_Is_bouton
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_via_type_II_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_II_bouton
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
temporal interpretation: axiom holds for all times
comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_by_via_type_II_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

synapsed_by_via_type_Ib_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

has postsynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
inverse of: has presynaptic terminal in
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: synapsed in
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

releases neurotransmitter
type: ObjectProperty
domain: UBERON_0000061
range: BFO_0000040
IAO_0000114: IAO_0000125
IAO_0000118: has neurotransmitter

synapsed_by_via_type_Is_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

has presynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000118: synapses in
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_via_type_III_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_III_bouton
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_by_via_type_III_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

synapsed to
type: ObjectProperty
sub property of: sends output to
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: part of
    some values from: CL_0000540
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))

dendrite synapsed in
type: ObjectProperty
sub property of: has postsynaptic terminal in
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal in
type: ObjectProperty
sub property of: overlaps
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has synapse in
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: IAO_0000125
IAO_0000115: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

has fasciculating neuron projection
type: ObjectProperty
sub property of: overlaps
domain: UBERON_0000122
range: Class
  union of: CL_0000540
  union of: Restriction
    on property: part of
    some values from: CL_0000540
IAO_0000114: IAO_0000125
IAO_0000115: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has fasciculating component
IAO_0000426: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

innervates
type: ObjectProperty
domain: UBERON_0000122
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
domain: BFO_0000004
range: BFO_0000004
IAO_0000114: IAO_0000125
IAO_0000115: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: connected to
IAO_0000232: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
temporal interpretation: axiom holds for all times

partially overlaps
type: ObjectProperty
sub property of: overlaps
IAO_0000114: IAO_0000125
IAO_0000115: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
IAO_0000116: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
IAO_0000118: proper overlaps
IAO_0000426: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
temporal interpretation: axiom holds for all times
in subset: ro-eco

derived by descent from
type: ObjectProperty
sub property of: evolutionarily related to
inverse of: has derived by descendant
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
IAO_0000118: ancestral_stucture_of
IAO_0000118: evolutionarily_descended_from

has derived by descendant
type: ObjectProperty
sub property of: evolutionarily related to
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: inverse of derived by descent from
in subset: defined by inverse

shares ancestor with
type: ObjectProperty
sub property of: evolutionarily related to
type: SymmetricProperty
type: TransitiveProperty
property chain axiom: derived by descent from
property chain axiom: has derived by descendant
IAO_0000114: IAO_0000125
IAO_0000115: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
IAO_0000232: Consider obsoleting and merging with child relation, 'in homology relationship with'
comment: VBO calls this homologous_to

serially homologous to
type: ObjectProperty
sub property of: evolutionarily related to
type: SymmetricProperty
type: TransitiveProperty
IAO_0000114: IAO_0000125

only in taxon
type: ObjectProperty
sub property of: in taxon
IAO_0000112: lactation SubClassOf 'only in taxon' some 'Mammalia'
IAO_0000114: IAO_0000125
IAO_0000115: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
IAO_0000116: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: OBI_0100026
property chain axiom: innervated by
property chain axiom: overlaps
property chain axiom: innervates
property chain axiom: continuous with
property chain axiom: connected to
property chain axiom: connects
property chain axiom: expressed in
property chain axiom: regulates
property chain axiom: has prototype
property chain axiom: capable of
property chain axiom: has developmental contribution from
property chain axiom: developmentally induced by
property chain axiom: results in developmental progression of
property chain axiom: has potential to develop into
property chain axiom: existence overlaps
property chain axiom: produces
property chain axiom: produced by
IAO_0000114: IAO_0000125
IAO_0000115: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
IAO_0000117: 0000-0001-9227-417X
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
has narrow synonym: life cycle stage of
in subset: ro-eco
comment: Connects a biological entity to its taxon of origin.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: IAO_0000125
IAO_0000115: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in subset: ro-eco

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: part of
  some values from: system
range: Restriction
  on property: part of
  some values from: system
property chain axiom:
  inverse of: connects
property chain axiom: connects
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000004
range: Restriction
  on property: part of
  some values from: system
IAO_0000112: The M8 connects Glasgow and Edinburgh
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

attached to part of
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: biomechanically related to
domain: UBERON_0000061
range: UBERON_0000061
property chain axiom: attached to
property chain axiom: part of
IAO_0000115: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
IAO_0000589: attached to part of (anatomical structure to anatomical structure)

Axiom
annotated source: attached to part of
annotated property: propertyChainAxiom
annotated target: attached to
annotated target: part of
RO_0002582: true

supplies
type: ObjectProperty
sub property of: connected to
IAO_0000115: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

drains
type: ObjectProperty
sub property of: connected to
IAO_0000115: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: IAO_0000125
IAO_0000115: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
temporal interpretation: axiom holds for all times
in subset: ro-eco

has phenotype
type: ObjectProperty
sub property of: has phenotype or disease
inverse of: phenotype of
domain: Class
  union of: BFO_0000031
  union of: OGMS_0000031
  union of: UBERON_0000465
range: UPHENO_0001001
IAO_0000114: IAO_0000125
IAO_0000115: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

phenotype of
type: ObjectProperty
type: FunctionalProperty
IAO_0000114: IAO_0000125
IAO_0000115: inverse of has phenotype
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse
in subset: ro-eco

develops from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: BFO_0000004
range: BFO_0000004
IAO_0000114: IAO_0000125
IAO_0000115: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: inverse of develops from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
in subset: defined by inverse

gene product of
type: ObjectProperty
sub property of: genomically related to
inverse of: has gene product
domain: BFO_0000004
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: BFO_0000002
range: Class
  union of: BFO_0000031
  union of: BFO_0000040
property chain axiom: ribosomal translation of
property chain axiom: transcribed from
IAO_0000114: IAO_0000125
IAO_0000115: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
IAO_0000116: We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has gene product
type: ObjectProperty
sub property of: genomically related to
domain: BFO_0000002
range: BFO_0000004
property chain axiom: transcribed to
property chain axiom: ribosomally translates to
IAO_0000112: every HOTAIR lncRNA is the gene product of some HOXC gene
IAO_0000112: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
IAO_0000114: IAO_0000125
IAO_0000115: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: BFO_0000002
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: UBERON_0000465
property chain axiom: part of
IAO_0000112: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
IAO_0000114: IAO_0000125
IAO_0000115: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
IAO_0000117: https://orcid.org/0000-0002-6601-2165

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
domain: Class
  union of: CL_0000000
  union of: UBERON_0010000
range: Class
  union of: CL_0000000
  union of: UBERON_0010000
IAO_0000114: IAO_0000125
IAO_0000115: Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000119: FBbt
is direct form of: develops from
has exact synonym: has developmental precursor
comment: TODO - add child relations from DOS

parasitoid of
type: ObjectProperty
sub property of: parasite of
inverse of: has parasitoid
IAO_0000115: A parasite that kills or sterilizes its host

has parasitoid
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of parasitoid of
in subset: defined by inverse

directly develops into
type: ObjectProperty
sub property of: develops into
IAO_0000114: IAO_0000125
IAO_0000115: inverse of directly develops from
IAO_0000118: developmental precursor of
in subset: defined by inverse

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
property chain axiom: has effector activity
property chain axiom: ends with
property chain axiom: directly regulates
IAO_0000115: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
IAO_0000117: https://orcid.org/0000-0001-7476-6306
IAO_0000117: https://orcid.org/0000-0002-3837-8864
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
IAO_0000115: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
is negative form of: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
IAO_0000115: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
is positive form of: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

has prototype
type: ObjectProperty
domain: Class
  union of: BFO_0000004
  union of: BFO_0000015
IAO_0000112: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
IAO_0000112: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
IAO_0000114: IAO_0000125
IAO_0000115: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
IAO_0000116: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
IAO_0000116: TODO: add homeomorphy axiom
IAO_0000116: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

capable of
type: ObjectProperty
sub property of: capable of part of
domain: BFO_0000004
range: BFO_0000015
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
IAO_0000115: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
IAO_0000115: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

obsolete actively participates in
type: ObjectProperty
IAO_0000115: OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: agent in
IAO_0100001: process has causal agent
comment: Obsoleted as the inverse property was obsoleted.
deprecated: true

obsolete has active participant
type: ObjectProperty
IAO_0000115: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has agent
IAO_0100001: causal agent in process
deprecated: true

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
IAO_0000114: IAO_0000125
IAO_0000115: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
IAO_0000117: https://orcid.org/0000-0002-6601-2165
temporal interpretation: axiom holds for all times

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: BFO_0000004
range: BFO_0000004
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: IAO_0000125
IAO_0000115: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: https://orcid.org/0000-0002-6601-2165
temporal interpretation: axiom holds for all times
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

Axiom
annotated source: adjacent to
annotated property: IAO_0000112
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

surrounds
type: ObjectProperty
sub property of: adjacent to
IAO_0000114: IAO_0000125
IAO_0000115: inverse of surrounded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165
temporal interpretation: axiom holds for all times
in subset: defined by inverse

temporally related to
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000003
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Allen's interval algebra
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
IAO_0000114: IAO_0000125
IAO_0000115: inverse of starts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Allen
in subset: ro-eco

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
IAO_0000112: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
IAO_0000114: IAO_0000125
IAO_0000115: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: started by
in subset: ro-eco

develops from part of
type: ObjectProperty
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

develops in
type: ObjectProperty
sub property of: developmentally preceded by
domain: UBERON_0001062
property chain axiom: directly develops from
property chain axiom: located in
IAO_0000114: IAO_0000125
IAO_0000115: x develops_in y if x is located in y whilst x is developing
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: EHDAA2
IAO_0000119: Jonathan Bard, EHDAA2

obligate parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.

facultative parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
IAO_0000114: IAO_0000125
IAO_0000115: inverse of ends with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: finished by
in subset: ro-eco

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: BFO_0000015
range: BFO_0000004
property chain axiom: starts with
property chain axiom: occurs in
IAO_0000114: IAO_0000125
IAO_0000115: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts with process that occurs in
in subset: ro-eco

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: BFO_0000015
range: BFO_0000004
property chain axiom: ends with
property chain axiom: occurs in
IAO_0000114: IAO_0000125
IAO_0000115: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends with process that occurs in
in subset: ro-eco

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: BFO_0000015
property chain axiom: starts with
IAO_0000114: IAO_0000125
IAO_0000115: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: consumes
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
property chain axiom: ends with
IAO_0000114: IAO_0000125
IAO_0000115: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: produces
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

stem parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)

root parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)

hemiparasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.

has component participant
type: ObjectProperty
sub property of: has participant
IAO_0000115: X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.
IAO_0000232: This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.
contributor: https://orcid.org/0000-0001-9625-1899

has exposure receptor
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
IAO_0000119: ExO:0000001

has exposure stressor
type: ObjectProperty
sub property of: has exposure stimulus
IAO_0000115: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
IAO_0000119: ExO:0000000

has exposure route
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
IAO_0000119: ExO:0000055

has exposure transport path
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A broad relationship between an exposure event or process and the course takes from the source to the target.
IAO_0000119: http://purl.obolibrary.org/obo/ExO_0000004

related via exposure to
type: ObjectProperty
sub property of: causally related to
domain: COB_0001000
IAO_0000115: Any relationship between an exposure event or process and any other entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.

over-expressed in
type: ObjectProperty
sub property of: expressed in
IAO_0000115: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.

under-expressed in
type: ObjectProperty
sub property of: expressed in
IAO_0000115: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

has active ingredient
type: ObjectProperty
sub property of: has part
inverse of: active ingredient in
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: Any portion of roundup 'has active ingredient' some glyphosate
IAO_0000115: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has exact synonym: has active substance
has related synonym: has active pharmaceutical ingredient

active ingredient in
type: ObjectProperty
sub property of: part of
IAO_0000115: inverse of has active ingredient
in subset: defined by inverse

connecting branch of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
inverse of: has connecting branch
IAO_0000112: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
IAO_0000115: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
nominally disjoint with: part of

has connecting branch
type: ObjectProperty
sub property of: in branching relationship with
IAO_0000115: inverse of connecting branch of
nominally disjoint with: has part
in subset: defined by inverse

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: UBERON_0001062
range: UBERON_0001062
property chain axiom: has part
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: IAO_0000125
IAO_0000115: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
IAO_0000114: IAO_0000125
IAO_0000115: inverse of has developmental contribution from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse

developmentally induced by
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally induces
domain: UBERON_0000465
range: UBERON_0000465
IAO_0000114: IAO_0000125
IAO_0000115: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: induced by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
IAO_0000119: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
IAO_0000119: GO:0001759
IAO_0000232: We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]

developmentally induces
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally induce
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of developmentally induced by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: BFO_0000002
range: BFO_0000002
IAO_0000114: IAO_0000125
IAO_0000115: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
IAO_0000116: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

has biological role
type: ObjectProperty
sub property of: has role
IAO_0000115: c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)

has application role
type: ObjectProperty
sub property of: has role
IAO_0000115: c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)

has chemical role
type: ObjectProperty
sub property of: has role
IAO_0000115: c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
IAO_0000115: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
IAO_0000115: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has related synonym: affects
in subset: valid for go gp2term

developmentally replaces
type: ObjectProperty
sub property of: developmentally preceded by
IAO_0000114: IAO_0000125
IAO_0000115: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
IAO_0000116: This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: replaces

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of developmentally preceded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

part of developmental precursor of
type: ObjectProperty
sub property of: developmentally succeeded by
property chain axiom: part of
property chain axiom: directly develops into
IAO_0000112: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165

ubiquitously expressed in
type: ObjectProperty
sub property of: expressed in
inverse of: ubiquitously expresses
IAO_0000114: IAO_0000125
IAO_0000115: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
IAO_0000116: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

expresses
type: ObjectProperty
sub property of: genomically related to
IAO_0000114: IAO_0000125
IAO_0000115: y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
IAO_0000114: IAO_0000125
IAO_0000115: inverse of ubiquiotously expressed in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: GO_0008150
range: UBERON_0001062
IAO_0000114: IAO_0000125
IAO_0000115: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
IAO_0000116: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in development of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000114: IAO_0000125
IAO_0000115: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in formation of anatomical entity
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
IAO_0000112: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
IAO_0000112: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in morphogenesis of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
IAO_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: IAO_0000125
IAO_0000115: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in maturation of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
IAO_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: IAO_0000125
IAO_0000115: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in disappearance of
type: ObjectProperty
sub property of: results in ending of
IAO_0000112: foramen ovale closure SubClassOf results in disappearance of foramen ovale
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: May be merged into parent relation

results in developmental regression of
type: ObjectProperty
sub property of: results in ending of
IAO_0000112: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: May be merged into parent relation

is treated by substance
type: ObjectProperty
sub property of: causally related to
inverse of: is substance that treats
IAO_0000115: Inverse of 'is substance that treats'
creator: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse

has habitat
type: ObjectProperty
sub property of: ecologically related to
domain: OBI_0100026
range: ENVO_01000254
IAO_0000112: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
IAO_0000114: IAO_0000428
IAO_0000115: x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
IAO_0000117: https://orcid.org/0000-0002-4366-3088
IAO_0000118: adapted for living in
in subset: ro-eco
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
IAO_0000115: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
is positive form of: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
IAO_0000115: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
is negative form of: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam

has exposure stimulus
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
contributor: https://orcid.org/0000-0001-6996-0040
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-8461-9745
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-06-05T17:35:04Z

evolutionary variant of
type: ObjectProperty
sub property of: evolutionarily related to
IAO_0000117: https://orcid.org/0000-0002-6601-2165

transports or maintains localization of
type: ObjectProperty
sub property of: related via localization to
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: regulates localization of
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
IAO_0000115: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
temporal interpretation: axiom holds for all times

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

results in acquisition of features of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
range: UBERON_0000061
IAO_0000112: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
IAO_0000115: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

evolutionarily related to
type: ObjectProperty
IAO_0000115: A relationship that holds via some environmental process
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.

ecologically related to
type: ObjectProperty
IAO_0000115: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in subset: ro-eco

confers advantage in
type: ObjectProperty
sub property of: ecologically related to
range: ENVO_01000254
IAO_0000116: An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: adapted for
in subset: ro-eco

mereotopologically related to
type: ObjectProperty
IAO_0000115: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
temporal interpretation: axiom holds for all times

developmentally related to
type: ObjectProperty
IAO_0000115: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

colocalizes with
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
IAO_0000115: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
in subset: valid for go gp2term

contributes to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of
IAO_0000112: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
IAO_0000112: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
IAO_0000112: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
IAO_0000116: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
in subset: valid for go gp2term

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
IAO_0000115: c enables p iff c is capable of p and c acts to execute p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in subset: valid for go gp2term

functionally related to
type: ObjectProperty
IAO_0000115: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
IAO_0000115: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

genomically related to
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000002
IAO_0000115: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
IAO_0000115: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: actively involved in
IAO_0000118: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: BFO_0000015
range: BFO_0000040
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
IAO_0000115: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: regulates levels of (process to entity)

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
IAO_0000115: inverse of enables
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
IAO_0000115: inverse of regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)
in subset: defined by inverse

negatively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse

positively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse

related via localization to
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000002
IAO_0000115: A relationship that holds via some process of localization
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is a grouping relation.

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

imports
type: ObjectProperty
sub property of: transports
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go ontology

results in transport along
type: ObjectProperty
sub property of: related via localization to
IAO_0000115: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in transport across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in
IAO_0000115: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go ontology

results in growth of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: 'pollen tube growth' results_in growth_of some 'pollen tube'
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to
IAO_0000112: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

exports
type: ObjectProperty
sub property of: transports
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go ontology

results in commitment to
type: ObjectProperty
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000112: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
IAO_0000115: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in determination of
type: ObjectProperty
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000115: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
IAO_0000112: An organism that is a member of a population of organisms
IAO_0000115: is member of is a mereological relation between a item and a collection.
IAO_0000118: is member of
IAO_0000118: member part of
IAO_0000119: SIO
temporal interpretation: axiom holds for all times

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
IAO_0000115: has member is a mereological relation between a collection and an item.
IAO_0000119: SIO
temporal interpretation: axiom holds for all times

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
IAO_0000115: inverse of has input
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse
in subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
IAO_0000115: inverse of has output
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse
in subset: ro-eco

formed as result of
type: ObjectProperty
sub property of: output of
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in structural organization of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in specification of
type: ObjectProperty
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000115: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in developmental induction of
type: ObjectProperty
sub property of: results in developmental progression of
IAO_0000115: p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has dendrite location
type: ObjectProperty
sub property of: overlaps
IAO_0000117: https://orcid.org/0000-0002-6601-2165
source: http://neurolex.org/wiki/Property:DendriteLocation

attached to
type: ObjectProperty
sub property of: connected to
sub property of: attached to part of
type: SymmetricProperty
IAO_0000115: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: attached to (anatomical structure to anatomical structure)
in subset: ro-eco

has muscle origin
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: UBERON_0000061
IAO_0000115: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle origin
annotated property: domain
annotated target: UBERON_0000061
comment: We need to import uberon muscle to create a stricter domain constraint

has muscle insertion
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: UBERON_0000061
IAO_0000115: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle insertion
annotated property: domain
annotated target: UBERON_0000061
IAO_0000116: We need to import uberon muscle into RO to use as a stricter domain constraint

derived from ancestral fusion of
type: ObjectProperty
sub property of: derived by descent from
IAO_0000112: false
IAO_0000114: IAO_0000428
IAO_0000115: x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
has broad synonym: has fused element
comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.

in branching relationship with
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000040
IAO_0000114: IAO_0000428
IAO_0000115: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
nominally disjoint with: part of

tributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
IAO_0000112: Deschutes River tributary_of Columbia River
IAO_0000112: inferior epigastric vein tributary_of external iliac vein
IAO_0000114: IAO_0000428
IAO_0000115: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: drains into
IAO_0000118: drains to
IAO_0000118: tributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Tributary
IAO_0000119: http://www.medindia.net/glossary/venous_tributary.htm
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
in subset: ro-eco

distributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
IAO_0000112: Deschutes River distributary_of Little Lava Lake
IAO_0000114: IAO_0000428
IAO_0000115: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: branch of
IAO_0000118: distributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Distributary
in subset: ro-eco
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes

anabranch of
type: ObjectProperty
sub property of: distributary of
sub property of:
  inverse of: tributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
IAO_0000114: IAO_0000428
IAO_0000115: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: anastomoses with
in subset: ro-eco

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
IAO_0000112: A lump of clay and a statue
IAO_0000115: x spatially_coextensive_with y if and inly if x and y have the same location
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

branching part of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
inverse of: has branching part
range: Restriction
  on property: has characteristic
  some values from: PATO_0000402
property chain axiom: distributary of
property chain axiom: main stem of
IAO_0000112: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
IAO_0000115: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

main stem of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
IAO_0000112: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'.
IAO_0000114: IAO_0000428
IAO_0000115: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

proper distributary of
type: ObjectProperty
sub property of: distributary of
IAO_0000114: IAO_0000428
IAO_0000115: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

proper tributary of
type: ObjectProperty
sub property of: tributary of
IAO_0000114: IAO_0000428
IAO_0000115: x proper_tributary_of y iff x tributary_of y and x does not originate from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: UBERON_0001062
range: UBERON_0001062
IAO_0000114: IAO_0000428
IAO_0000115: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally induce
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has direct input
type: ObjectProperty
sub property of: has input
property chain axiom: starts with
IAO_0000112: 'protein catabolic process' SubClassOf has_direct_input some protein
IAO_0000114: IAO_0000428
IAO_0000115: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly consumes
IAO_0000232: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'

obsolete has indirect input
type: ObjectProperty
IAO_0000114: IAO_0000428
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

obsolete has direct output
type: ObjectProperty
IAO_0000112: translation SubClassOf has_direct_output some protein
IAO_0000114: IAO_0000428
IAO_0000115: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly produces
deprecated: true

obsolete has indirect output
type: ObjectProperty
property chain axiom: causally upstream of
property chain axiom: obsolete has direct output
IAO_0000114: IAO_0000428
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: IAO_0000428
IAO_0000115: inverse of upstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: IAO_0000428
IAO_0000117: https://orcid.org/0000-0002-6601-2165

obsolete directly activates
type: ObjectProperty
IAO_0100001: directly positively regulates
comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'.
deprecated: true

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
IAO_0000115: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly activates
is indirect form of: positively regulates

obsolete directly inhibits
type: ObjectProperty
IAO_0100001: directly negatively regulates
comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'.
deprecated: true

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
IAO_0000115: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly inhibits
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
IAO_0000115: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: IAO_0000115
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
has db xref: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
IAO_0000115: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
IAO_0000115: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is direct form of: causally upstream of

provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: has output
property chain axiom: has input
IAO_0000115: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly provides input for
IAO_0000119: causal-relations
IAO_0000589: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of or within, positive effect
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
IAO_0000114: IAO_0000428
IAO_0000115: transitive form of directly_provides_input_for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
IAO_0000589: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
property chain axiom: part of
IAO_0000115: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: influences (processual)
has related synonym: affects

differs in
type: ObjectProperty
IAO_0000116: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: This is an exploratory relation

differs in attribute of
type: ObjectProperty
sub property of: differs in
range: Class
  union of: BFO_0000004
  union of: BFO_0000015
IAO_0000117: https://orcid.org/0000-0002-6601-2165

differs in attribute
type: ObjectProperty
sub property of: differs in
range: BFO_0000020
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
IAO_0000115: inverse of causally upstream of or within
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
in subset: defined by inverse

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is positive form of: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is negative form of: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
IAO_0000115: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
IAO_0000115: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: executes activity in
has exact synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: IAO_0000115
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: https://orcid.org/0000-0002-7073-9172

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
IAO_0000115: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has exact synonym: in pairwise interaction with
in subset: ro-eco

genetically interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
IAO_0000116: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
IAO_0000115: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: binds
IAO_0000118: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: interacts with on organism level
in subset: ro-eco

trophically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000112: lions trophically interact with the zebras that they eat
IAO_0000115: An interaction relationship in which the partners are related via a feeding relationship.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

preys on
type: ObjectProperty
sub property of: trophically interacts with
inverse of: preyed upon by
IAO_0000112: A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
IAO_0000112: Baleen whale preys on krill
IAO_0000115: An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
IAO_0000117: https://orcid.org/0000-0001-7134-3324
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-3138-4118
IAO_0000118: is subject of predation interaction with
IAO_0000118: preys upon
in subset: ro-eco

symbiotically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
type: SymmetricProperty
property chain axiom: partner in
property chain axiom: is symbiosis
property chain axiom:
  inverse of: partner in
IAO_0000112: whales symbiotically interact with the barnacles that attach to them
IAO_0000115: A biotic interaction in which the two organisms live together in more or less intimate association.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
in subset: ro-eco

commensually interacts with
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is commensalism
property chain axiom:
  inverse of: partner in
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
in subset: ro-eco

mutualistically interacts with
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is mutualism
property chain axiom:
  inverse of: partner in
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
in subset: ro-eco

interacts with via parasite-host interaction
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is parasitism
property chain axiom:
  inverse of: partner in
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: This relation groups a pair of inverse relations, parasite of and parasitized by
in subset: ro-eco

parasite of
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: has host
inverse of: parasitized by
property chain axiom: subject participant in
property chain axiom: is parasitism
property chain axiom:
  inverse of: target participant in
IAO_0000112: Pediculus humanus capitis parasite of human
IAO_0000115: A parasite-host relationship where an organism benefits at the expense of another.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: parasitizes
has exact synonym: direct parasite of
in subset: ro-eco

parasitized by
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: host of
IAO_0000115: Inverse of parasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has parasite
IAO_0000118: parasitised by
has exact synonym: directly parasitized by
in subset: ro-eco

participates in a abiotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
IAO_0000112: Porifiera attaches to substrate
IAO_0000115: A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has related synonym: semibiotically interacts with
in subset: ro-eco

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is kinase activity
property chain axiom: has direct input
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: BFO_0000040
range: BFO_0000040
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
has exact synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: BFO_0000040
range: BFO_0000040
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly inhibits
has exact synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: BFO_0000040
range: BFO_0000040
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly activates
has exact synonym: molecularly increases activity of

transmitted by
type: ObjectProperty
sub property of: ecologically related to
IAO_0000112: all dengue disease transmitted by some mosquito
IAO_0000115: A relationship that holds between a disease and organism
IAO_0000116: Add domain and range constraints
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has symptom
type: ObjectProperty
sub property of: has phenotype
domain: OGMS_0000031
IAO_0000115: A relation that holds between a disease or an organism and a phenotype
IAO_0000117: https://orcid.org/0000-0002-6601-2165

host of
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
in subset: ro-eco

has host
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000115: X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

pollinates
type: ObjectProperty
sub property of: mutualistically interacts with
inverse of: pollinated by
IAO_0000112: Bees pollinate Flowers
IAO_0000116: This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: is subject of pollination interaction with
in subset: ro-eco

pollinated by
type: ObjectProperty
sub property of: mutualistically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has polinator
IAO_0000118: is target of pollination interaction with
in subset: ro-eco

acquires nutrients from
type: ObjectProperty
sub property of: biotically interacts with
inverse of: provides nutrients for
IAO_0000115: Inverse of provides nutrients for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
in subset: ro-eco

preyed upon by
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000115: inverse of preys on
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has predator
IAO_0000118: is target of predation interaction with
in subset: defined by inverse
in subset: ro-eco

is vector for
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: has vector
IAO_0000112: Anopheles is a vector for Plasmodium
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
in subset: ro-eco

has vector
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

partner in
type: ObjectProperty
sub property of: participates in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target

subject participant in
type: ObjectProperty
sub property of: partner in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.

target participant in
type: ObjectProperty
sub property of: partner in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is symbiosis
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is commensalism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is mutualism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is parasitism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: https://orcid.org/0000-0002-6601-2165

provides nutrients for
type: ObjectProperty
sub property of: biotically interacts with
IAO_0000115: A biotic interaction where a material entity provides nutrition for an organism.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

eats
type: ObjectProperty
sub property of: biotically interacts with
IAO_0000115: A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: is subject of eating interaction with
in subset: ro-eco

is eaten by
type: ObjectProperty
sub property of: biotically interacts with
IAO_0000115: Inverse of eats
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: eaten by
IAO_0000118: is target of eating interaction with
in subset: ro-eco

is evidence for
type: ObjectProperty
sub property of: related via evidence or inference to
inverse of: has evidence
IAO_0000115: A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

composed primarily of
type: ObjectProperty
sub property of: has part
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
IAO_0000115: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
temporal interpretation: axiom holds for all times
in subset: ro-eco

child nucleus of
type: ObjectProperty
sub property of: developmentally preceded by
domain: GO_0005634
range: GO_0005634
IAO_0000112: ABal nucleus child nucleus of ABa nucleus (in C elegans)
IAO_0000115: c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.

child nucleus of in hermaphrodite
type: ObjectProperty
sub property of: child nucleus of
IAO_0000115: A child nucleus relationship in which the cells are part of a hermaphroditic organism
IAO_0000117: https://orcid.org/0000-0002-6601-2165

child nucleus of in male
type: ObjectProperty
sub property of: child nucleus of
IAO_0000115: A child nucleus relationship in which the cells are part of a male organism
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has part that occurs in
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000004
property chain axiom: has part
property chain axiom: occurs in
IAO_0000115: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has part
annotated target: occurs in
is a defining property chain axiom: true

ubiquitinates
type: ObjectProperty
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is ubiquitination
property chain axiom: has direct input
IAO_0000115: An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is ubiquitination
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
IAO_0000116: See notes for inverse relation
IAO_0000117: https://orcid.org/0000-0002-6601-2165

sends output to
type: ObjectProperty
sub property of: connected to
IAO_0000116: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

relation between physical entity and a process or stage
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000003
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
property chain axiom: existence starts at end of
IAO_0000115: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

existence starts with
type: ObjectProperty
sub property of: existence starts during
IAO_0000115: x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
IAO_0000115: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts and ends during
type: ObjectProperty
sub property of: existence starts during
sub property of: existence ends during
IAO_0000115: x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has exact synonym: exists during
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
property chain axiom: existence ends at start of
IAO_0000115: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends with
type: ObjectProperty
sub property of: existence ends during
IAO_0000115: x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

transformation of
type: ObjectProperty
sub property of: develops from
type: TransitiveProperty
IAO_0000115: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
IAO_0000117: https://orcid.org/0000-0002-6601-2165

immediate transformation of
type: ObjectProperty
sub property of: directly develops from
sub property of: transformation of
IAO_0000115: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is direct form of: transformation of

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: preceded by
property chain axiom: simultaneous with
property chain axiom: existence starts at end of
property chain axiom:
  inverse of: existence starts at end of
IAO_0000115: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally succeeded by
property chain axiom: precedes
property chain axiom: simultaneous with
property chain axiom: existence ends at start of
property chain axiom:
  inverse of: existence ends at start of
IAO_0000115: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
IAO_0000115: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000003
range: BFO_0000003
IAO_0000115: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165

towards
type: ObjectProperty
sub property of: depends on
IAO_0000115: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
IAO_0000116: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
sub property of: has participant
IAO_0000112: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
IAO_0000115: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has intermediate product
in subset: ro-eco

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000002
range: BFO_0000002
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

determined by
type: ObjectProperty
sub property of: part of
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
domain: system
range: BFO_0000040
IAO_0000112: A coral reef environment is determined by a particular coral reef
IAO_0000115: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
IAO_0000116: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/24330602
IAO_0000589: determined by (system to material entity)
creator: https://orcid.org/0000-0002-4366-3088
creator: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

determines
type: ObjectProperty
sub property of: causally influences
IAO_0000115: inverse of determined by
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: determines (material entity to system)
in subset: defined by inverse
in subset: ro-eco

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between entities
domain: system
range: BFO_0000040
property chain axiom: determined by
property chain axiom: part of
IAO_0000115: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

Axiom
annotated source: determined by part of
annotated property: propertyChainAxiom
annotated target: determined by
annotated target: part of
RO_0002582: true

transcribed from
type: ObjectProperty
sub property of: genomically related to
inverse of: transcribed to
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: Class
  union of: BFO_0000031
  union of: BFO_0000040
IAO_0000115: x is transcribed from y if and only if x is synthesized from template y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

transcribed to
type: ObjectProperty
sub property of: genomically related to
IAO_0000115: inverse of transcribed from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
in subset: defined by inverse

ribosomal translation of
type: ObjectProperty
sub property of: genomically related to
inverse of: ribosomally translates to
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: Class
  union of: BFO_0000031
  union of: BFO_0000040
IAO_0000115: x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

ribosomally translates to
type: ObjectProperty
sub property of: genomically related to
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: Class
  union of: BFO_0000031
  union of: BFO_0000040
IAO_0000115: inverse of ribosomal translation of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

sequentially related to
type: ObjectProperty
domain: sequentially ordered entity
range: sequentially ordered entity
IAO_0000115: A relation that holds between two entities that have the property of being sequences or having sequences.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000232: The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
cites as authority: 006650.abstract

sequentially adjacent to
type: ObjectProperty
sub property of: does not overlap sequence of
IAO_0000112: Every UTR is adjacent to a CDS of the same transcript
IAO_0000112: Two consecutive DNA residues are sequentially adjacent
IAO_0000112: Two exons on a processed transcript that were previously connected by an intron are adjacent
IAO_0000115: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

has start sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is start sequence of
type: TransitiveProperty
IAO_0000112: Every CDS has as a start sequence the start codon for that transcript
IAO_0000115: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: started by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is start sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
IAO_0000115: inverse of has start sequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in subset: defined by inverse

has end sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is end sequence of
type: TransitiveProperty
IAO_0000112: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
IAO_0000115: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ended by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is end sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
IAO_0000115: inverse of has end sequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in subset: defined by inverse

is consecutive sequence of
type: ObjectProperty
sub property of: has subsequence
IAO_0000115: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
IAO_0000116: In the SO paper, this was defined as an instance-type relation
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is sequentially aligned with
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
IAO_0000112: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
IAO_0000115: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

bounds sequence of
type: ObjectProperty
sub property of: sequentially related to
inverse of: is bound by sequence of
type: TransitiveProperty
IAO_0000112: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
IAO_0000115: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

is bound by sequence of
type: ObjectProperty
sub property of: sequentially related to
type: TransitiveProperty
IAO_0000115: inverse of bounds sequence of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract
in subset: defined by inverse

has subsequence
type: ObjectProperty
sub property of: has part
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of
type: TransitiveProperty
IAO_0000115: x has subsequence y iff all of the sequence parts of y are sequence parts of x
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: contains
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is subsequence of
type: ObjectProperty
sub property of: part of
sub property of: is bound by sequence of
sub property of: overlaps sequence of
type: TransitiveProperty
IAO_0000115: inverse of has subsequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: contained by
cites as authority: 006650.abstract
in subset: defined by inverse

overlaps sequence of
type: ObjectProperty
sub property of: overlaps
sub property of: sequentially related to
type: SymmetricProperty
property chain axiom: has subsequence
property chain axiom: is subsequence of
IAO_0000115: x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

does not overlap sequence of
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
IAO_0000115: x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: disconnected from
cites as authority: 006650.abstract

is upstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
IAO_0000115: inverse of downstream of sequence of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

is downstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
IAO_0000115: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

is immediately downstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of
IAO_0000112: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is direct form of: is downstream of sequence of
cites as authority: 006650.abstract

is immediately upstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of
IAO_0000112: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: inverse of immediately downstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

has skeleton
type: ObjectProperty
sub property of: has part
inverse of: skeleton of
type: AsymmetricProperty
type: IrreflexiveProperty
domain: UBERON_0000061
range: UBERON_0000465
IAO_0000112: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
IAO_0000115: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has supporting framework
IAO_0000232: The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).

Axiom
annotated source: has skeleton
annotated property: range
annotated target: UBERON_0000465
IAO_0000116: This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.

results in ending of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

hyperparasite of
type: ObjectProperty
sub property of: has host
inverse of: hyperparasitized by
property chain axiom: parasite of
IAO_0000115: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000116: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
has narrow synonym: hyperparasitoid of
has related synonym: epiparasite of
in subset: ro-eco

hyperparasitized by
type: ObjectProperty
sub property of: host of
property chain axiom: parasitized by
IAO_0000115: inverse of hyperparasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has related synonym: has epiparasite
has related synonym: has hyperparasite
has related synonym: hyperparasitoidized by
in subset: defined by inverse
in subset: ro-eco

allelopath of
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: has allelopath
IAO_0000115: A relationship between organisms where one organism is influenced by the biochemicals produced by another.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://en.wikipedia.org/wiki/Allelopathy
in subset: ro-eco
comment: Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth, survival or reproduction of other organisms in its vicinity.
see also: x is an allelopath of y if x produces one or more biochemicals that influence the growth, survival, and reproduction of y

pathogen of
type: ObjectProperty
sub property of: has host
inverse of: has pathogen
IAO_0000115: Inverse of has pathogen
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

has pathogen
type: ObjectProperty
sub property of: host of
IAO_0000115: A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

has evidence
type: ObjectProperty
sub property of: related via evidence or inference to
IAO_0000115: inverse of is evidence for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/25052702
in subset: defined by inverse
in subset: ro-eco
comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in movement of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: BFO_0000002
range: BFO_0000002
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
IAO_0000115: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
domain: UBERON_0000061
range: UBERON_0000061
IAO_0000115: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.

has muscle antagonist
type: ObjectProperty
sub property of: biomechanically related to
IAO_0000115: m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Wikipedia:Antagonist_(muscle)

has branching part
type: ObjectProperty
sub property of: has part
sub property of: in branching relationship with
type: TransitiveProperty
IAO_0000115: inverse of branching part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse
in subset: ro-eco

conduit for
type: ObjectProperty
sub property of: overlaps
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: UBERON:cjm
IAO_0000232: This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
in subset: ro-eco

lumen of
type: ObjectProperty
sub property of: part of
range: BFO_0000040
IAO_0000115: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: BFO_0000141
IAO_0000115: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

has modifier
type: ObjectProperty
domain: BFO_0000020
range: BFO_0000020
IAO_0000115: A relation that holds between an attribute or a qualifier and another attribute.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
IAO_0000232: This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
in subset: ro-eco

participates in a biotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
domain: OBI_0100026
range: OBI_0100026
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

skeleton of
type: ObjectProperty
sub property of: part of
domain: UBERON_0000061
range: UBERON_0000061
IAO_0000115: inverse of has skeleton
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: defined by inverse

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
IAO_0000115: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
is direct form of: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

existence starts at end of
type: ObjectProperty
sub property of: existence starts during or after
IAO_0000115: holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
IAO_0000115: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in closure of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000116: p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.

results in breakdown of
type: ObjectProperty
sub property of: has input
IAO_0000115: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p

results in synthesis of
type: ObjectProperty
sub property of: results in formation of anatomical entity

results in assembly of
type: ObjectProperty
sub property of: results in formation of anatomical entity
sub property of: results in organization of
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in catabolism of
type: ObjectProperty
sub property of: results in breakdown of
IAO_0000115: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.

results in disassembly of
type: ObjectProperty
sub property of: results in breakdown of
sub property of: results in organization of

results in remodeling of
type: ObjectProperty
sub property of: has input
sub property of: results in organization of

results in organization of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c

existence ends at start of
type: ObjectProperty
sub property of: existence ends during or before
IAO_0000115: holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000040
range: BFO_0000015
IAO_0000115: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations

capable of inhibiting or preventing pathological process
type: ObjectProperty
sub property of: capable of negatively regulating
IAO_0000112: pazopanib -> pathological angiogenesis
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
IAO_0000118: treats
IAO_0000119: causal-relations
IAO_0000232: The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.

Axiom
annotated source: capable of inhibiting or preventing pathological process
annotated property: IAO_0000118
annotated target: treats
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship

capable of upregulating or causing pathological process
type: ObjectProperty
sub property of: capable of positively regulating
IAO_0000112: benzene -> cancer [CHEBI]
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
IAO_0000118: causes disease
IAO_0000119: causal-relations

is substance that treats
type: ObjectProperty
sub property of: capable of inhibiting or preventing pathological process
IAO_0000115: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
IAO_0000118: treats
IAO_0000119: causal-relations

is marker for
type: ObjectProperty
sub property of: correlated with
IAO_0000115: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
IAO_0000116: May be ceded to OBI

process has causal agent
type: ObjectProperty
sub property of: causally related to
IAO_0000115: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

obsolete related via dependence to
type: ObjectProperty
IAO_0000115: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
deprecated: true

correlated with
type: ObjectProperty
IAO_0000115: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
IAO_0000232: Groups both positive and negative correlation

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
IAO_0000112: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
IAO_0000115: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
comment: In the Gene Ontology association model, this corresponds to the With/From field

has model
type: ObjectProperty
inverse of: has role in modeling
IAO_0000115: Inverse of is-model-of

related via evidence or inference to
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is a grouping relation.

visits
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: visited by

visited by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

visits flowers of
type: ObjectProperty
sub property of: visits
inverse of: has flowers visited by

has flowers visited by
type: ObjectProperty
sub property of: visited by

lays eggs in
type: ObjectProperty
sub property of: parasite of
sub property of: visits
inverse of: has eggs laid in by

has eggs laid in by
type: ObjectProperty
sub property of: parasitized by
sub property of: visited by

kills
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: is killed by
IAO_0000119: https://github.com/jhpoelen/eol-globi-data/issues/143

is killed by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
IAO_0000115: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
is positive form of: directly regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
IAO_0000115: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
is negative form of: directly regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

ectoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has ectoparasite
IAO_0000115: A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
IAO_0000119: Types

has ectoparasite
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of ectoparasite of
in subset: defined by inverse

endoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has endoparasite
IAO_0000119: Types
IAO_0000119: A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
has related synonym: lives inside of

has endoparasite
type: ObjectProperty
sub property of: parasitized by

mesoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has mesoparasite
IAO_0000115: A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite

has mesoparasite
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of mesoparasite of
in subset: defined by inverse

intercellular endoparasite of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intercellular endoparasite
IAO_0000115: A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
IAO_0000119: Types

has intercellular endoparasite
type: ObjectProperty
sub property of: has endoparasite
IAO_0000115: inverse of intercellular endoparasite of
in subset: defined by inverse

intracellular endoparasite of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intracellular endoparasite
IAO_0000115: A sub-relation of endoparasite-of in which the parasite inhabits host cells.
IAO_0000119: Types

has intracellular endoparasite
type: ObjectProperty
sub property of: has endoparasite
IAO_0000115: inverse of intracellular endoparasite of
in subset: defined by inverse

co-roosts with
type: ObjectProperty
sub property of: ecologically co-occurs with
type: SymmetricProperty
IAO_0000115: Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
IAO_0000119: Communal roosting

reservoir host of
type: ObjectProperty
sub property of: host of
inverse of: has reservoir host
IAO_0000112: An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s.
IAO_0000115: A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host.
IAO_0000119: v13071356
contributor: https://orcid.org/0000-0002-3120-4802
contributor: https://orcid.org/0000-0003-3138-4118
comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts.

has reservoir host
type: ObjectProperty
sub property of: has host
IAO_0000112: An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s.
IAO_0000115: inverse of reservoir host of
in subset: defined by inverse

produces
type: ObjectProperty
inverse of: produced by
domain: BFO_0000040
range: BFO_0000040
property chain axiom:
  inverse of: occurs in
property chain axiom: has output
IAO_0000114: IAO_0000125
IAO_0000115: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in subset: ro-eco
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.

produced by
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000114: IAO_0000125
IAO_0000115: a produced_by b iff some process that occurs_in b has_output a.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in subset: ro-eco

represses expression of
type: ObjectProperty
sub property of: directly negatively regulates activity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

increases expression of
type: ObjectProperty
sub property of: directly positively regulates activity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

has role in modeling
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
IAO_0000115: A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
IAO_0000117: https://orcid.org/0000-0002-1048-5019
IAO_0000118: is used to study
comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate.

causes or contributes to condition
type: ObjectProperty
sub property of: causally related to
IAO_0000112: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
IAO_0000116: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

causes condition
type: ObjectProperty
sub property of: causes or contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.

contributes to condition
type: ObjectProperty
sub property of: causes or contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.

contributes to severity of condition
type: ObjectProperty
sub property of: contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
IAO_0000118: contributes to expressivity of condition

contributes to frequency of condition
type: ObjectProperty
sub property of: contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
IAO_0000118: contributes to penetrance of condition

ameliorates condition
type: ObjectProperty
sub property of: contributes to severity of condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
IAO_0000118: is preventative for condition
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

correlated with condition
type: ObjectProperty
sub property of: correlated with
IAO_0000115: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

exacerbates condition
type: ObjectProperty
sub property of: contributes to severity of condition
IAO_0000115: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.

condition ameliorated by
type: ObjectProperty
sub property of: causally related to
IAO_0000115: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.

condition exacerbated by
type: ObjectProperty
sub property of: causally related to
IAO_0000115: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.

condition has genetic basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is genetic basis for condition
domain: BFO_0000017
range: Class
  union of: BFO_0000015
  union of: BFO_0000019
  union of: BFO_0000040
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:38:20Z

has material basis in gain of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal gain of function germline mutation of in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:45:20Z

has material basis in loss of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal loss of function germline mutation of in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:45:37Z

has material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:45:54Z

has material basis in somatic mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal somatic mutation in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:46:07Z

has major susceptibility factor
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal susceptibility factor for
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:46:26Z

has partial material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation partially giving rise to
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:46:57Z

has primary input or output
type: ObjectProperty
sub property of: has participant
IAO_0000115: p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-12-13T11:26:17Z
in subset: valid for go ontology

has primary output
type: ObjectProperty
sub property of: has output
sub property of: has primary input or output
IAO_0000115: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-12-13T11:26:32Z
in subset: valid for go ontology

Axiom
annotated source: has primary output
annotated property: IAO_0000115
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: GOC:dph
has db xref: GOC:kva
has db xref: GOC:pt
comment: PMID:27812932

has primary input
type: ObjectProperty
sub property of: has input
sub property of: has primary input or output
IAO_0000115: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-12-13T11:26:56Z
in subset: valid for go ontology

Axiom
annotated source: has primary input
annotated property: IAO_0000115
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: GOC:dph
has db xref: GOC:kva
has db xref: GOC:pt
comment: PMID:27812932

is genetic basis for condition
type: ObjectProperty
sub property of: is basis for realizable
range: BFO_0000017
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:53:08Z

is causal gain of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:55:51Z

is causal loss of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:56:06Z

is causal germline mutation in
type: ObjectProperty
sub property of: causes condition
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:56:40Z

is causal somatic mutation in
type: ObjectProperty
sub property of: causes condition
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:57:07Z

is causal susceptibility factor for
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:57:43Z

is causal germline mutation partially giving rise to
type: ObjectProperty
sub property of: contributes to condition
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:58:43Z

realizable has basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is basis for realizable
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:20:01Z

is basis for realizable
type: ObjectProperty
sub property of: causally related to
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:20:29Z

disease has basis in
type: ObjectProperty
sub property of: realizable has basis in
sub property of: causal relationship with disease as subject
domain: OGMS_0000031
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:26:47Z

disease has basis in dysfunction of
type: ObjectProperty
sub property of: disease has basis in
range: UBERON_0000465
IAO_0000115: A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
IAO_0000589: disease has basis in dysfunction of (disease to anatomical structure)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:29:32Z

disease has basis in disruption of
type: ObjectProperty
sub property of: disease has basis in
range: BFO_0000015
IAO_0000115: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
IAO_0000589: disease has basis in disruption of (disease to process)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:37:52Z

disease has basis in feature
type: ObjectProperty
sub property of: has phenotype
sub property of: disease has basis in
domain: OGMS_0000031
range: Class
  union of: OGMS_0000031
  union of: UPHENO_0001001
IAO_0000115: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:46:07Z

causal relationship with disease as subject
type: ObjectProperty
sub property of: causally related to
sub property of: disease relationship
domain: OGMS_0000031
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:50:54Z

disease causes disruption of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: OGMS_0000031
range: BFO_0000015
property chain axiom: part of
property chain axiom: disease causes dysfunction of
property chain axiom: capable of
IAO_0000115: A relationship between a disease and a process where the disease process disrupts the execution of the process.
IAO_0000589: disease causes disruption of (disease to process)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:51:09Z

disease causes dysfunction of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: OGMS_0000031
range: UBERON_0000465
property chain axiom: part of
IAO_0000589: disease causes dysfunction of (disease to anatomical entity)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:58:20Z

disease has location
type: ObjectProperty
sub property of: disease relationship
domain: OGMS_0000031
range: BFO_0000004
range: Class
  union of: UBERON_0000465
  union of: UBERON_0000466
IAO_0000115: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
IAO_0000116: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
IAO_0000232: This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T04:06:02Z

disease has inflammation site
type: ObjectProperty
sub property of: disease has location
domain: OGMS_0000031
range: BFO_0000004
range: Class
  union of: UBERON_0000465
  union of: UBERON_0000466
IAO_0000115: A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:37:31Z

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000017
range: BFO_0000040
property chain axiom: realized in response to
property chain axiom: has input
IAO_0000115: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:45:49Z

disease has feature
type: ObjectProperty
sub property of: disease relationship
domain: OGMS_0000031
range: Class
  union of: OGMS_0000031
  union of: UPHENO_0001001
IAO_0000115: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:50:53Z

disease arises from alteration in structure
type: ObjectProperty
sub property of: disease has basis in
range: UBERON_0000061
IAO_0000115: A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:58:44Z

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
IAO_0000115: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
is positive form of: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:30Z
in subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
is negative form of: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:51Z
in subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
IAO_0000115: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
is positive form of: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:14Z
in subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
IAO_0000115: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
is negative form of: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:22Z
in subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
is negative form of: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
is positive form of: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

DEPRECATED inheres in
type: ObjectProperty
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
deprecated: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

has driver
type: ObjectProperty
IAO_0000115: A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.
contributor: https://orcid.org/0000-0001-8910-9851

has disease driver
type: ObjectProperty
sub property of: has driver
IAO_0000115: A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.
contributor: https://orcid.org/0000-0001-8910-9851

epiphyte of
type: ObjectProperty
sub property of: symbiotically interacts with
inverse of: has epiphyte
IAO_0000115: An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
IAO_0000119: https://en.wikipedia.org/wiki/Epiphyte

has epiphyte
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000115: inverse of epiphyte of
in subset: defined by inverse

kleptoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: kleptoparasitized by
IAO_0000115: A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
IAO_0000119: https://en.wikipedia.org/wiki/Kleptoparasitism

kleptoparasitized by
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of kleptoparasite of
in subset: defined by inverse

creates habitat for
type: ObjectProperty
sub property of: ecologically related to
domain: OBI_0100026
range: OBI_0100026
IAO_0000115: An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.

ecologically co-occurs with
type: ObjectProperty
sub property of: ecologically related to
type: SymmetricProperty
domain: OBI_0100026
range: OBI_0100026
IAO_0000115: An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.

lays eggs on
type: ObjectProperty
sub property of: visits
inverse of: has eggs laid on by
IAO_0000115: An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.

has eggs laid on by
type: ObjectProperty
sub property of: visited by
IAO_0000115: inverse of lays eggs on

has roost
type: ObjectProperty
sub property of: has habitat
domain: OBI_0100026
range: ENVO_01000739
IAO_0000112: Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)
IAO_0000115: x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.
contributor: https://orcid.org/0000-0002-2908-3327
date: 2023-01-18T14:28:21Z
in subset: ro-eco
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.

symbiotrophically interacts with
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000112: frog symbiotrophically interacts with the pitcher plant it lives inside of
IAO_0000115: A trophic interaction in which one organism acquires nutrients through a symbiotic relationship with another organism
contributor: https://orcid.org/0000-0002-2908-3327
date: 2023-07-17T14:39:56Z
in subset: ro-eco

trophic parasite of
type: ObjectProperty
sub property of: symbiotrophically interacts with
IAO_0000112: tapeworm is trophic parasite of the cow it lives inside of
IAO_0000115: A symbiotrophic interaction in which one organism acquires nutrients through a parasitic relationship with another organism
contributor: https://orcid.org/0000-0002-2908-3327
date: 2023-07-17T14:41:07Z
in subset: ro-eco

has substance added
type: ObjectProperty
type: IrreflexiveProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: muffin 'has substance added' some 'baking soda'
IAO_0000114: IAO_0000428
IAO_0000115: "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
IAO_0000116: The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

has substance removed
type: ObjectProperty
type: IrreflexiveProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: 'egg white' 'has substance removed' some 'egg yolk'
IAO_0000114: IAO_0000428
IAO_0000115: "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

immersed in
type: ObjectProperty
type: IrreflexiveProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: sardines 'immersed in' some 'oil and mustard'
IAO_0000114: IAO_0000428
IAO_0000115: "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

has consumer
type: ObjectProperty
domain: BFO_0000040
range: OBI_0100026
IAO_0000112: sardine has consumer some homo sapiens
IAO_0000114: IAO_0000428
IAO_0000115: 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

has primary substance added
type: ObjectProperty
sub property of: has substance added
type: IrreflexiveProperty
IAO_0000112: bread 'has primary substance added' some 'flour'
IAO_0000114: IAO_0000428
IAO_0000115: 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

assay measures characteristic
type: ObjectProperty
inverse of: characteristic measured by assay
domain: OBI_0000070
range: BFO_0000020
IAO_0000112: A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material.
IAO_0000115: A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic.
contributor: https://orcid.org/0000-0002-8844-9165
date: 2023-05-23T15:24:15Z

characteristic measured by assay
type: ObjectProperty
domain: BFO_0000020
range: OBI_0000070
IAO_0000115: Inverse of 'assay measures characteristic'
contributor: https://orcid.org/0000-0002-8844-9165
date: 2023-05-23T15:29:50Z

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000017
range: BFO_0000015
property chain axiom: realized in
property chain axiom: causally downstream of
IAO_0000112: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
IAO_0000112: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
IAO_0000112: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
IAO_0000115: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: https://orcid.org/0000-0001-6996-0040
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-7073-9172
contributor: https://orcid.org/0000-0002-8461-9745
has exact synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: hasExactSynonym
annotated target: triggered by process
has db xref: https://orcid.org/0000-0002-6601-2165

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: BFO_0000031
range: BFO_0000004
property chain axiom: characteristic of
property chain axiom: is concretized as
IAO_0000112: Genetic information generically depend on molecules of DNA.
IAO_0000112: The novel *War and Peace* generically depends on this copy of the novel.
IAO_0000112: The pattern shared by chess boards generically depends on any chess board.
IAO_0000112: The score of a symphony g-depends on a copy of the score.
IAO_0000112: This pdf file generically depends on this server.
IAO_0000115: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
IAO_0000119: [072-ISO]
has exact synonym: g-depends on

is carrier of
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000031
property chain axiom: concretizes
property chain axiom: has characteristic
IAO_0000112: Molecules of DNA are carriers of genetic information.
IAO_0000112: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
IAO_0000112: This hard drive is carrier of these data items.
IAO_0000115: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
IAO_0000119: [072-ISO]

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

regulates quantity of
type: ObjectProperty
sub property of: causally influences
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly regulates activity of
type: ObjectProperty
sub property of: regulates activity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

decreases by repression quantity of
type: ObjectProperty
sub property of: indirectly negatively regulates quantity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

increases by expression quantity of
type: ObjectProperty
sub property of: indirectly positively regulates quantity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

directly positively regulates quantity of
type: ObjectProperty
sub property of: directly regulates quantity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A has an activity that directly positively regulates the quantity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

directly negatively regulates quantity of
type: ObjectProperty
sub property of: directly regulates quantity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A has an activity that directly negatively regulates the quantity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly positively regulates activity of
type: ObjectProperty
sub property of: indirectly regulates activity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: indirectly activates

destabilizes quantity of
type: ObjectProperty
sub property of: directly negatively regulates quantity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
IAO_0000115: An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

stabilizes quantity of
type: ObjectProperty
sub property of: directly positively regulates quantity of
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
IAO_0000115: An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly negatively regulates activity of
type: ObjectProperty
sub property of: indirectly regulates activity of
IAO_0000115: The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: indirectly inhibits

directly regulates quantity of
type: ObjectProperty
sub property of: regulates quantity of
IAO_0000115: The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly regulates quantity of
type: ObjectProperty
sub property of: regulates quantity of
IAO_0000115: The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly negatively regulates quantity of
type: ObjectProperty
sub property of: indirectly regulates quantity of
IAO_0000115: The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly positively regulates quantity of
type: ObjectProperty
sub property of: indirectly regulates quantity of
IAO_0000115: The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

has small molecule regulator
type: ObjectProperty
sub property of: has participant
inverse of: is small molecule regulator of
IAO_0000115: a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-04-22T20:27:26Z

has small molecule activator
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule activator of
IAO_0000115: a relation between a process and a continuant, in which the process is activated by the small molecule continuant
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-04-22T20:28:37Z

has small molecule inhibitor
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule inhibitor of
IAO_0000115: a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-04-22T20:28:54Z

acts on population of
type: ObjectProperty
sub property of: has participant
IAO_0000115: p acts on population of c iff c' is a collection, has members of type c, and p has participant c
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-08T17:21:33Z
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

is small molecule regulator of
type: ObjectProperty
sub property of: capable of regulating
IAO_0000115: a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-24T13:15:17Z

is small molecule activator of
type: ObjectProperty
sub property of: capable of positively regulating
sub property of: is small molecule regulator of
IAO_0000115: a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-24T13:15:26Z

is small molecule inhibitor of
type: ObjectProperty
sub property of: capable of negatively regulating
sub property of: is small molecule regulator of
IAO_0000115: a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-24T13:15:35Z

results in adhesion of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-08-27T08:13:59Z

results in fusion of
type: ObjectProperty
sub property of: results in organization of
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2021-02-26T07:28:29Z
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

constitutively upstream of
type: ObjectProperty
sub property of: causally upstream of, positive effect
IAO_0000115: p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:01:01Z
in subset: valid for go annotation extension
in subset: valid for gocam

removes input for
type: ObjectProperty
sub property of: causally upstream of, negative effect
IAO_0000115: p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:06:20Z
in subset: valid for go annotation extension
in subset: valid for gocam

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
IAO_0000115: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
IAO_0000115: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:08:01Z

positively regulates in another organism
type: ObjectProperty
sub property of: regulates in another organism
IAO_0000115: x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
is positive form of: regulates in another organism
contributor: https://orcid.org/0000-0003-1813-6857
creation date: 2023-10-12T10:02:28Z
has exact synonym: positively regulates in other organism
in subset: valid for go ontology

negatively regulates in another organism
type: ObjectProperty
sub property of: regulates in another organism
IAO_0000115: x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
is negative form of: regulates in another organism
contributor: https://orcid.org/0000-0003-1813-6857
creation date: 2023-10-12T10:02:42Z
has exact synonym: negatively regulates in other organism
in subset: valid for go ontology

has synaptic IO in region
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:26:52Z
has exact synonym: has synaptic input or output in

receives synaptic input in region
type: ObjectProperty
sub property of: has postsynaptic terminal in
sub property of: has synaptic IO in region
property chain axiom: part of
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:42:23Z

sends synaptic output to region
type: ObjectProperty
sub property of: has presynaptic terminal in
sub property of: has synaptic IO in region
property chain axiom: part of
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:45:06Z

has synaptic IO throughout
type: ObjectProperty
sub property of: has synaptic IO in region
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:52:19Z

receives synaptic input throughout
type: ObjectProperty
sub property of: receives synaptic input in region
sub property of: has synaptic IO throughout
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:55:36Z

sends synaptic output throughout
type: ObjectProperty
sub property of: sends synaptic output to region
sub property of: has synaptic IO throughout
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:57:27Z

has sensory dendrite in
type: ObjectProperty
sub property of: has dendrite location
domain: CL_0000101
property chain axiom: part of
IAO_0000115: Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-20T12:10:09Z
has exact synonym: has sensory dendrite location
has exact synonym: has sensory terminal in
has exact synonym: has sensory terminal location

receives synaptic input from neuron
type: ObjectProperty
sub property of: synapsed by
inverse of: sends synaptic output to cell
IAO_0000115: A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2021-05-26T08:40:18Z

sends synaptic output to cell
type: ObjectProperty
sub property of: synapsed to
IAO_0000115: A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2021-05-26T08:41:07Z
comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.

synapses restricted to region
type: ObjectProperty
sub property of: has synaptic IO in region
property chain axiom: part of
IAO_0000112: An optic lobe intrinsic neuron has its synapses restricted to optic lobe neuropil.
IAO_0000115: A relationship between a neuron and a region, where all of the functionally relevant input and output synapses are in that region.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2023-08-17T12:17:24Z
has exact synonym: intrinsic to
comment: This relation may still be used if a very small number of synapses fall slightly outside the boundaries of the region, but any class using this relation should not have another restriction using this relation to another non-overlapping region.

disease has infectious agent
type: ObjectProperty
sub property of: disease has basis in
IAO_0000115: A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.
created by: https://orcid.org/0000-0001-5208-3432

has exemplar data
type: ObjectProperty
sub property of: topObjectProperty
inverse of: exemplar data of
property chain axiom: subcluster of
IAO_0000112: transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])
IAO_0000115: A relation between a material entity and some data in which the data is taken as exemplifying the material entity.
IAO_0000116: C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C.
IAO_0000117: https://orcid.org/0000-0002-5260-9315
IAO_0000232: This relation is not meant to capture the relation between occurrents and data.

exemplar data of
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000117: https://orcid.org/0000-0002-5260-9315

subcluster of
type: ObjectProperty
sub property of: part of
type: TransitiveProperty
IAO_0000115: A relation between a group and another group it is part of but does not fully constitute.
IAO_0000116: X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
IAO_0000117: https://orcid.org/0000-0001-7258-9596
IAO_0000232: This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics.

has characterizing marker set
type: ObjectProperty
domain: CL_0000000
IAO_0000112: 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1').
IAO_0000112: transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3.
IAO_0000115: A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
IAO_0000116: C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
IAO_0000232: This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context.
contributor: https://orcid.org/0000-0001-7258-9596
has exact synonym: has marker gene combination
has exact synonym: has marker signature set

different in magnitude relative to
type: ObjectProperty
domain: PATO_0000001
range: PATO_0000001
IAO_0000115: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: different in magnitude relative to
annotated property: IAO_0000115
annotated target: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

increased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: PATO_0000001
range: PATO_0000001
IAO_0000115: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.

Axiom
annotated source: increased in magnitude relative to
annotated property: IAO_0000115
annotated target: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

decreased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: PATO_0000001
range: PATO_0000001
IAO_0000115: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.

Axiom
annotated source: decreased in magnitude relative to
annotated property: IAO_0000115
annotated target: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

similar in magnitude relative to
type: ObjectProperty
IAO_0000115: q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: similar in magnitude relative to
annotated property: IAO_0000115
annotated target: q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

has relative magnitude
type: ObjectProperty

has cross section
type: ObjectProperty
IAO_0000115: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

Axiom
annotated source: has cross section
annotated property: IAO_0000115
annotated target: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
has db xref: https://orcid.org/0000-0002-6601-2165

reciprocal of
type: ObjectProperty
IAO_0000115: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

Axiom
annotated source: reciprocal of
annotated property: IAO_0000115
annotated target: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
has db xref: https://orcid.org/0000-0002-6601-2165

has high plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: CL_0000000
IAO_0000112: 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
IAO_0000115: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
contributor: https://orcid.org/0000-0003-1617-8244
contributor: https://orcid.org/0000-0003-1940-6740

Axiom
annotated source: has high plasma membrane amount
annotated property: IAO_0000115
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
has db xref: PMID:19243617

has low plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: CL_0000000
IAO_0000112: 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
IAO_0000115: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
contributor: https://orcid.org/0000-0003-1617-8244
contributor: https://orcid.org/0000-0003-1940-6740

Axiom
annotated source: has low plasma membrane amount
annotated property: IAO_0000115
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
has db xref: PMID:19243617

has phenotype or disease
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.
contributor: https://orcid.org/0000-0002-7463-6306
date: 2021-11-05T17:30:14Z

has disease
type: ObjectProperty
sub property of: has phenotype or disease
IAO_0000115: A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
contributor: https://orcid.org/0000-0002-7463-6306
date: 2021-11-05T17:30:44Z

has exposure medium
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.
IAO_0000119: ExO:0000083
creator: https://orcid.org/0000-0002-7463-6306
date: 2021-12-14T20:41:45Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000112: A diagnostic testing device utilizes a specimen.
IAO_0000115: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
IAO_0000232: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
IAO_0000232: See github ticket https://github.com/oborel/obo-relations/issues/497
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-2620-0345
creation date: 2021-11-08T12:00:00Z
has broad synonym: utilizes

positively correlated with
type: ObjectProperty
sub property of: correlated with
type: SymmetricProperty
IAO_0000115: A relation between entities in which one increases or decreases as the other does the same.
IAO_0000118: directly correlated with
contributor: https://orcid.org/0000-0003-1909-9269

negatively correlated with
type: ObjectProperty
sub property of: correlated with
type: SymmetricProperty
type: IrreflexiveProperty
IAO_0000115: A relation between entities in which one increases as the other decreases.
IAO_0000118: inversely correlated with
contributor: https://orcid.org/0000-0003-1909-9269

contains measured amount
type: ObjectProperty
domain: OBI_0000967
range: COB_0000121
IAO_0000112: anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.
IAO_0000115: A relation between a container and measurement datum that specifies the actual amount of material in the container.
contributor: https://orcid.org/0000-0002-2999-0103
contributor: 0000-0002-5714-991X

has maximum capacity
type: ObjectProperty
domain: OBI_0000967
range: COB_0000121
IAO_0000112: anticoagulant-containing test tube has maximum capacity 10 ml.
IAO_0000115: A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume.
contributor: https://orcid.org/0000-0002-2999-0103
contributor: 0000-0002-5714-991X

owns
type: ObjectProperty
inverse of: is owned by
IAO_0000112: biobank organization owns a specimen
IAO_0000112: hospital owns a laboratory facility
IAO_0000115: A primitive relation that holds between entities x and y in which y is at x's full disposal.
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-1834-3856
contributor: https://orcid.org/0000-0003-1909-9269
description: This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal.
creation date: 2023-03-29T16:57:03Z

is owned by
type: ObjectProperty
IAO_0000112: freezer is owned by a biobank organization
IAO_0000115: Inverse of the owns relation.
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-1834-3856
contributor: https://orcid.org/0000-0003-1909-9269
creation date: 2023-03-29T17:06:06Z
in subset: defined by inverse

collected during
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000003
IAO_0000112: A thorax specimen was collected during the larval stage.
IAO_0000112: An oyster was collected during low tide.
IAO_0000115: A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent.
contributor: https://orcid.org/0000-0002-8844-9165
date: 2023-09-13T04:12:32Z

is myristoyltransferase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000115: Helper relation for OWL definition of RO:0018002 myristoylates
contributor: https://orcid.org/0000-0003-4423-4370

myristoylates
type: ObjectProperty
sub property of: molecularly interacts with
inverse of: myristoylated by
property chain axiom: capable of
property chain axiom: is myristoyltransferase activity
property chain axiom: has direct input
IAO_0000115: A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input
conforms to: ObjectPropertyDefinedByInteractionProcess
contributor: https://orcid.org/0000-0003-4423-4370

myristoylated by
type: ObjectProperty
IAO_0000115: inverse of myristoylates
contributor: https://orcid.org/0000-0003-4423-4370

is agonist of
type: ObjectProperty
sub property of: directly positively regulates activity of
IAO_0000112: mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)
IAO_0000115: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor
creator: https://orcid.org/0000-0003-4423-4370

is inverse agonist of
type: ObjectProperty
sub property of: directly negatively regulates activity of
IAO_0000112: pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)
IAO_0000115: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level
creator: https://orcid.org/0000-0003-4423-4370

is antagonist of
type: ObjectProperty
sub property of: directly negatively regulates activity of
IAO_0000112: tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)
IAO_0000115: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level
creator: https://orcid.org/0000-0003-4423-4370

chemical relationship
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical.
creator: https://orcid.org/0000-0003-4423-4370

is direct conjugate base of
type: ObjectProperty
sub property of: is deprotonated form of
inverse of: is direct conjugate acid of
IAO_0000112: pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)
IAO_0000115: A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B.
is direct form of: is deprotonated form of
creator: https://orcid.org/0000-0003-4423-4370

is direct conjugate acid of
type: ObjectProperty
sub property of: is protonated form of
IAO_0000112: neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)
IAO_0000115: A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B.
is direct form of: is protonated form of
creator: https://orcid.org/0000-0003-4423-4370

is deprotonated form of
type: ObjectProperty
sub property of: chemical relationship
inverse of: is protonated form of
type: TransitiveProperty
IAO_0000112: (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons.
IAO_0000115: A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
creator: https://orcid.org/0000-0003-4423-4370
has db xref: obo:chebi#is_conjugate_base_of

is protonated form of
type: ObjectProperty
sub property of: chemical relationship
type: TransitiveProperty
IAO_0000112: (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons.
IAO_0000115: A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
creator: https://orcid.org/0000-0003-4423-4370
has db xref: obo:chebi#is_conjugate_acid_of

is matched small molecular pair with
type: ObjectProperty
sub property of: chemical relationship
type: SymmetricProperty
IAO_0000112: phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol.
IAO_0000115: A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
creator: https://orcid.org/0000-0003-4423-4370
date: 2023-02-28T18:53:32Z
has exact synonym: is MMP with
has exact synonym: is matched molecular pair with

Axiom
annotated source: is matched small molecular pair with
annotated property: IAO_0000115
annotated target: A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
source: ddr.21045
source: jm200452d
source: Matched molecular pair analysis

is tautomer of
type: ObjectProperty
sub property of: chemical relationship
type: SymmetricProperty
IAO_0000112: 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
IAO_0000115: Two chemicals are tautomers if they can be readily interconverted. This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
creator: https://orcid.org/0000-0003-4423-4370
date: 2023-03-18T23:49:31Z
has db xref: obo:chebi#is_tautomer_of
has exact synonym: is desmotrope of

Axiom
annotated source: is tautomer of
annotated property: IAO_0000112
annotated target: 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.

is substitutent group from
type: ObjectProperty
sub property of: chemical relationship
IAO_0000112: carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
IAO_0000115: Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.
creator: https://orcid.org/0000-0003-4423-4370
date: 2023-03-18T23:49:31Z
has db xref: obo:chebi#is_substituent_group_from

Axiom
annotated source: is substitutent group from
annotated property: IAO_0000112
annotated target: carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)

has functional parent
type: ObjectProperty
sub property of: chemical relationship
IAO_0000112: hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
IAO_0000115: Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
creator: https://orcid.org/0000-0003-4423-4370
date: 2023-03-18T23:49:31Z
has db xref: obo:chebi#has_functional_parent

Axiom
annotated source: has functional parent
annotated property: IAO_0000112
annotated target: hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)

is enantiomer of
type: ObjectProperty
sub property of: chemical relationship
type: SymmetricProperty
IAO_0000112: dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
IAO_0000115: Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
creator: https://orcid.org/0000-0003-4423-4370
date: 2023-03-18T23:49:31Z
has db xref: obo:chebi#is_enantiomer_of
has exact synonym: is optical isomer of

Axiom
annotated source: is enantiomer of
annotated property: IAO_0000112
annotated target: dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
comment: CHEBI_48557

has parent hydride
type: ObjectProperty
sub property of: chemical relationship
IAO_0000112: pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
IAO_0000115: Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.
creator: https://orcid.org/0000-0003-4423-4370
date: 2023-03-18T23:49:31Z
has db xref: obo:chebi#has_parent_hydride

Axiom
annotated source: has parent hydride
annotated property: IAO_0000112
annotated target: pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000015
range: PATO_0000001
property chain axiom: regulates
IAO_0000115: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
IAO_0000115: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
IAO_0000115: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

confers susceptibility to condition
type: ObjectProperty
sub property of: contributes to condition
IAO_0000115: Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.
created by: https://orcid.org/0000-0002-4142-7153

vessel supplies blood to
type: ObjectProperty
sub property of: supplies
domain: UBERON_0001981
range: UBERON_0000061
IAO_0000112: brachial artery vessel supplies blood to brachialis muscle
IAO_0000115: x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-02-01T10:09:22Z

vessel drains blood from
type: ObjectProperty
sub property of: drains
domain: UBERON_0001981
range: UBERON_0000061
IAO_0000112: cystic vein vessel drains blood from gallbladder
IAO_0000115: x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-02-01T10:09:41Z

directly supplies and drains
type: ObjectProperty
sub property of: supplies
sub property of: drains
domain: UBERON_0001982
range: UBERON_0000061
IAO_0000112: alveolar capillary directly supplies and drains some alveolus
IAO_0000115: x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-02-01T10:09:59Z

is neuron
type: ObjectProperty
domain: CL_0000540
IAO_0000115: This property only applies to neurons
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-10-23T14:34:52Z

is anatomical entity
type: ObjectProperty
domain: UBERON_0001062
IAO_0000115: This property only applies to anatomical entities.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-10-29T09:55:07Z

has numerator
type: ObjectProperty
sub property of: has part
domain: PATO_0001470
range: PATO_0000001
IAO_0000115: A relationship between a ratio or proportion and its dividend.
contributor: https://orcid.org/0000-0001-8314-2140
has exact synonym: has dividend

has denominator
type: ObjectProperty
sub property of: has part
domain: PATO_0001470
range: PATO_0000001
IAO_0000115: A relationship between a ratio or proportion and its divisor.
contributor: https://orcid.org/0000-0001-8314-2140
has exact synonym: has divisor

has allelopath
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000115: inverse of allelopath of
IAO_0000117: https://orcid.org/0009-0005-5515-1230

provides clinical information for
type: ObjectProperty
sub property of: is marker for
IAO_0000112: A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer.
IAO_0000115: A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'. Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

diagnostic for
type: ObjectProperty
sub property of: provides clinical information for
IAO_0000112: A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue.
IAO_0000112: An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia.
IAO_0000115: A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

monitors status of
type: ObjectProperty
sub property of: provides clinical information for
IAO_0000112: Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression.
IAO_0000115: A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Usage note: The status of 'd' refers to disease progression/remission or treatment response. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

indicates response to
type: ObjectProperty
sub property of: indicates clinical effect of
IAO_0000112: The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1.
IAO_0000115: A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

predicts effect of
type: ObjectProperty
sub property of: indicates clinical effect of
IAO_0000112: The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug.
IAO_0000115: A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug. Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes: - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

prognostic for
type: ObjectProperty
sub property of: provides clinical information for
IAO_0000112: A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer.
IAO_0000115: A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

assesses toxicity of
type: ObjectProperty
sub property of: indicates clinical effect of
IAO_0000112: As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys.
IAO_0000115: A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

indicates risk of developing
type: ObjectProperty
sub property of: provides clinical information for
IAO_0000112: The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer.
IAO_0000115: A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

indicates clinical effect of
type: ObjectProperty
sub property of: is marker for
IAO_0000112: An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy.
IAO_0000115: A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. Usage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'. Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

monitors effect of
type: ObjectProperty
sub property of: indicates clinical effect of
IAO_0000112: The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers.
IAO_0000115: A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

monitors exposure to
type: ObjectProperty
sub property of: indicates clinical effect of
IAO_0000112: The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke.
IAO_0000115: A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'.
IAO_0000117: https://orcid.org/0000-0001-5809-9523
created by: https://orcid.org/0000-0001-5809-9523
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. Usage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers: - 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest; - 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent; - 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent. Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.

disease relationship
type: ObjectProperty
IAO_0000115: This relation groups relations between diseases and any other kind of entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-09-26T00:00:32Z

results in changes to anatomical or cellular structure
type: ObjectProperty
sub property of: has participant
IAO_0000115: p has anatomical participant c iff p has participant c, and c is an anatomical entity
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-09-26T01:08:58Z

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
IAO_0000115: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
IAO_0000116: TODO: Add homeomorphy axiom
is homeomorphic for: BFO_0000002
is homeomorphic for: BFO_0000003
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: ECO:0000041
has db xref: SO:similar_to
has exact synonym: sameness
has exact synonym: similar to
has related synonym: correspondence
has related synonym: resemblance

Axiom
annotated source: in similarity relationship with
annotated property: IAO_0000115
annotated target: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
has db xref: HOM_0000000
has db xref: BGEE:curator

Axiom
annotated source: in similarity relationship with
annotated property: hasRelatedSynonym
annotated target: correspondence
has db xref: http://dx.doi.org/10.1007/BF02814479

in homology relationship with
type: ObjectProperty
sub property of: shares ancestor with
sub property of: in similarity relationship with
type: SymmetricProperty
property disjoint with: in homoplasy relationship with
IAO_0000115: Similarity that results from common evolutionary origin.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: homologous to
comment: This broad definition encompasses all the working definitions proposed so far in the literature.

Axiom
annotated source: in homology relationship with
annotated property: IAO_0000115
annotated target: Similarity that results from common evolutionary origin.
has db xref: bies.950180611
has db xref: jmor.1051730307
has db xref: http://dx.doi.org/10.1007/BF02814480
has db xref: HOM_0000001

in homoplasy relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
IAO_0000115: Similarity that results from independent evolution.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: homoplasous to
has related synonym: analogy

Axiom
annotated source: in homoplasy relationship with
annotated property: IAO_0000115
annotated target: Similarity that results from independent evolution.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000002

in homocracy relationship with
type: ObjectProperty
sub property of: evolutionarily related to
sub property of: in similarity relationship with
type: SymmetricProperty
IAO_0000115: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: ECO:0000075
has exact synonym: homocracous to
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.

Axiom
annotated source: in homocracy relationship with
annotated property: IAO_0000115
annotated target: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: s00427-003-0301-4
has db xref: http://dx.doi.org/10.1186/1742-9994-2-15
has db xref: HOM_0000003

in convergence relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
IAO_0000115: Homoplasy that involves different underlying mechanisms or structures.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has related synonym: analogy
comment: Convergence usually implies a notion of adaptation.

Axiom
annotated source: in convergence relationship with
annotated property: IAO_0000115
annotated target: Homoplasy that involves different underlying mechanisms or structures.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000004

in parallelism relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
IAO_0000115: Homoplasy that involves homologous underlying mechanisms or structures.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: parallel evolution
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.

Axiom
annotated source: in parallelism relationship with
annotated property: IAO_0000115
annotated target: Homoplasy that involves homologous underlying mechanisms or structures.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000005

in structural homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
IAO_0000115: Homology that is defined by similarity with regard to selected structural parameters.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: ECO:0000071
has db xref: MI:2163
has exact synonym: structural homologous to
has related synonym: idealistic homology

Axiom
annotated source: in structural homology relationship with
annotated property: IAO_0000115
annotated target: Homology that is defined by similarity with regard to selected structural parameters.
has db xref: j.jhevol.2006.11.014
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000006
has db xref: ISBN:0123195837

in historical homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
IAO_0000115: Homology that is defined by common descent.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has broad synonym: homology
has db xref: ECO:0000080
has db xref: RO_proposed_relation:homologous_to
has db xref: SO:0000330
has db xref: SO:0000853
has db xref: SO:0000857
has db xref: SO:homologous_to
has db xref: TAO:homologous_to
has exact synonym: cladistic homology
has exact synonym: historical homologous to
has exact synonym: phylogenetic homology
has exact synonym: taxic homology
has related synonym: true homology

Axiom
annotated source: in historical homology relationship with
annotated property: IAO_0000115
annotated target: Homology that is defined by common descent.
has db xref: S0169-5347(97)01125-7
has db xref: HOM_0000007
has db xref: ISBN:0123195837

in biological homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
IAO_0000115: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: ECO:0000067
has exact synonym: biological homologous to
has related synonym: transformational homology
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.

Axiom
annotated source: in biological homology relationship with
annotated property: IAO_0000115
annotated target: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
has db xref: S0169-5347(97)01125-7
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000008

in reversal relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
IAO_0000115: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: atavism
has exact synonym: rudiment
has related synonym: reversion

Axiom
annotated source: in reversal relationship with
annotated property: IAO_0000115
annotated target: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000009

in syntenic homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
IAO_0000115: Structural homology that is detected by similarity in content and organization between chromosomes.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: MeSH:Synteny
has db xref: SO:0000860
has db xref: SO:0005858
has exact synonym: syntenic homologous to
has related synonym: synteny

Axiom
annotated source: in syntenic homology relationship with
annotated property: IAO_0000115
annotated target: Structural homology that is detected by similarity in content and organization between chromosomes.
has db xref: HOM_0000010
has db xref: MeSH:Synteny

in paralogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
property disjoint with: in orthology relationship with
IAO_0000115: Historical homology that involves genes that diverged after a duplication event.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: SO:0000854
has db xref: SO:0000859
has db xref: SO:paralogous_to
has exact synonym: paralogous to

Axiom
annotated source: in paralogy relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves genes that diverged after a duplication event.
has db xref: S0168-9525(00)02005-9
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000011
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in syntenic paralogy relationship with
type: ObjectProperty
sub property of: in syntenic homology relationship with
sub property of: in paralogy relationship with
type: SymmetricProperty
IAO_0000115: Paralogy that involves sets of syntenic blocks.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: syntenic paralogous to
has related synonym: duplicon
has related synonym: paralogon

Axiom
annotated source: in syntenic paralogy relationship with
annotated property: IAO_0000115
annotated target: Paralogy that involves sets of syntenic blocks.
has db xref: 1471-213X-7-100
has db xref: HOM_0000012
has db xref: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y

in syntenic orthology relationship with
type: ObjectProperty
sub property of: in syntenic homology relationship with
type: SymmetricProperty
IAO_0000115: Syntenic homology that involves chromosomes of different species.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: syntenic orthologous to

Axiom
annotated source: in syntenic orthology relationship with
annotated property: IAO_0000115
annotated target: Syntenic homology that involves chromosomes of different species.
has db xref: gr.6380007
has db xref: HOM_0000013

in partial homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
IAO_0000115: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: fractional homology
has exact synonym: partial homologous to
has exact synonym: segmental homology
has related synonym: mixed homology
has related synonym: modular homology
has related synonym: partial correspondence
has related synonym: percent homology

Axiom
annotated source: in partial homology relationship with
annotated property: IAO_0000115
annotated target: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
has db xref: HOM_0000014
has db xref: ISBN:0123195837
has db xref: ISBN:978-0471984931

in protein structural homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
IAO_0000115: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: MeSH:Structural_Homology,_Protein
has exact synonym: protein structural homologous to

Axiom
annotated source: in protein structural homology relationship with
annotated property: IAO_0000115
annotated target: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
has db xref: 0022-2836(76)90195-9
has db xref: HOM_0000015

in non functional homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
property disjoint with: in equivalogy relationship with
IAO_0000115: Structural homology that involves a pseudogenic feature and its functional ancestor.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has broad synonym: pseudogene
has db xref: SO:non_functional_homolog_of
has exact synonym: non functional homologous to

Axiom
annotated source: in non functional homology relationship with
annotated property: IAO_0000115
annotated target: Structural homology that involves a pseudogenic feature and its functional ancestor.
has db xref: HOM_0000016
has db xref: SO:non_functional_homolog_of

in orthology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves genes that diverged after a speciation event.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: ECO:00000060
has db xref: SO:0000855
has db xref: SO:0000858
has db xref: SO:orthologous_to
has exact synonym: orthologous to
comment: The term is sometimes also used for anatomical structures.

Axiom
annotated source: in orthology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves genes that diverged after a speciation event.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: S0168-9525(00)02005-9
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000017
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in xenology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: xenologous to
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).

Axiom
annotated source: in xenology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
has db xref: S0168-9525(00)02005-9
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000018

in 1 to 1 homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves two members sharing no other homologs in the lineages considered.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: 1 to 1 homologous to
has exact synonym: 1:1 homology
has exact synonym: one-to-one homology

Axiom
annotated source: in 1 to 1 homology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves two members sharing no other homologs in the lineages considered.
has db xref: HOM_0000019
has db xref: BGEE:curator

in 1 to 1 orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in 1 to 1 homology relationship with
type: SymmetricProperty
IAO_0000115: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: 1 to 1 orthologous to
has exact synonym: 1:1 orthology
has exact synonym: one-to-one orthology

Axiom
annotated source: in 1 to 1 orthology relationship with
annotated property: IAO_0000115
annotated target: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: HOM_0000020
has db xref: homology method.html

in ohnology relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
IAO_0000115: Paralogy that results from a whole genome duplication event.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: ohnologous to
has related synonym: homoeology

Axiom
annotated source: in ohnology relationship with
annotated property: IAO_0000115
annotated target: Paralogy that results from a whole genome duplication event.
has db xref: http://dx.doi.org/10.1038/75560
has db xref: HOM_0000022

in in-paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
property disjoint with: in out-paralogy relationship with
IAO_0000115: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: in-paralogous to
has exact synonym: inparalogy
has exact synonym: symparalogy

Axiom
annotated source: in in-paralogy relationship with
annotated property: IAO_0000115
annotated target: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000023

in out-paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
IAO_0000115: Paralogy that results from a duplication preceding a given speciation event.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: alloparalogy
has exact synonym: out-paralogous to
has exact synonym: outparalogy

Axiom
annotated source: in out-paralogy relationship with
annotated property: IAO_0000115
annotated target: Paralogy that results from a duplication preceding a given speciation event.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000024

in pro-orthology relationship with
type: ObjectProperty
sub property of: in 1 to many orthology relationship with
type: SymmetricProperty
IAO_0000115: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: pro-orthologous to

Axiom
annotated source: in pro-orthology relationship with
annotated property: IAO_0000115
annotated target: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
has db xref: scdb.1999.0338
has db xref: nrg2099
has db xref: HOM_0000025

in semi-orthology relationship with
type: ObjectProperty
sub property of: in 1 to many orthology relationship with
type: SymmetricProperty
IAO_0000115: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: semi-orthologous to
comment: The converse of pro-orthologous.

Axiom
annotated source: in semi-orthology relationship with
annotated property: IAO_0000115
annotated target: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
has db xref: scdb.1999.0338
has db xref: nrg2099
has db xref: HOM_0000026

in serial homology relationship with
type: ObjectProperty
sub property of: in iterative homology relationship with
type: SymmetricProperty
IAO_0000115: Iterative homology that involves structures arranged along the main body axis.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: serial homologous to
has related synonym: homonomy

Axiom
annotated source: in serial homology relationship with
annotated property: IAO_0000115
annotated target: Iterative homology that involves structures arranged along the main body axis.
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000027

in heterochronous homology relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
IAO_0000115: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: heterochronous homologous to
has exact synonym: heterochrony

Axiom
annotated source: in heterochronous homology relationship with
annotated property: IAO_0000115
annotated target: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
has db xref: HOM_0000028
has db xref: ISBN:978-0674639416

in paedomorphorsis relationship with
type: ObjectProperty
sub property of: in heterochronous homology relationship with
type: SymmetricProperty
property disjoint with: in peramorphosis relationship with
IAO_0000115: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: juvenification
has exact synonym: pedomorphosis

Axiom
annotated source: in paedomorphorsis relationship with
annotated property: IAO_0000115
annotated target: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
has db xref: Pedomorphosis
has db xref: HOM_0000029
has db xref: ISBN:978-0674639416

in peramorphosis relationship with
type: ObjectProperty
sub property of: in heterochronous homology relationship with
type: SymmetricProperty
IAO_0000115: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in peramorphosis relationship with
annotated property: IAO_0000115
annotated target: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
has db xref: Peramorphosis
has db xref: HOM_0000030

in progenesis relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
IAO_0000115: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in progenesis relationship with
annotated property: IAO_0000115
annotated target: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
has db xref: Progenesis
has db xref: HOM_0000031
has db xref: ISBN:978-0674639416

in neoteny relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
IAO_0000115: Paedomorphosis that is produced by a retardation of somatic development.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: juvenilization
has exact synonym: neotenous to

Axiom
annotated source: in neoteny relationship with
annotated property: IAO_0000115
annotated target: Paedomorphosis that is produced by a retardation of somatic development.
has db xref: Neoteny
has db xref: HOM_0000032
has db xref: ISBN:978-0674639416

in mimicry relationship with
type: ObjectProperty
sub property of: in convergence relationship with
type: SymmetricProperty
IAO_0000115: Convergence that results from co-evolution usually involving an evolutionary arms race.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: mimicrous to

Axiom
annotated source: in mimicry relationship with
annotated property: IAO_0000115
annotated target: Convergence that results from co-evolution usually involving an evolutionary arms race.
has db xref: Mimicry
has db xref: HOM_0000033

in 1 to many orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in 1 to many homology relationship with
type: SymmetricProperty
IAO_0000115: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: 1 to many orthologous to
has exact synonym: 1:many orthology
has exact synonym: one-to-many orthology
has related synonym: co-orthology
has related synonym: many to 1 orthology

Axiom
annotated source: in 1 to many orthology relationship with
annotated property: IAO_0000115
annotated target: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
has db xref: 415741a
has db xref: HOM_0000034
has db xref: homology method.html

in many to many homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves two members of a larger set of homologs.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: many to many homologous to
has exact synonym: many-to-many homology
has exact synonym: many:many homology

Axiom
annotated source: in many to many homology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves two members of a larger set of homologs.
has db xref: msp002
has db xref: HOM_0000036

in 1 to many homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: 1 to many homologous to
has exact synonym: one-to-many homology
has related synonym: 1:many homology

Axiom
annotated source: in 1 to many homology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
has db xref: HOM_0000037
has db xref: BGEE:curator

in apomorphy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
property disjoint with: in plesiomorphy relationship with
IAO_0000115: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: apomorphous to
has related synonym: synapomorphy

Axiom
annotated source: in apomorphy relationship with
annotated property: IAO_0000115
annotated target: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
has db xref: HOM_0000042
has db xref: ISBN:978-0252068140

in plesiomorphy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that is based on distant shared ancestry.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: plesiomorphous to
has related synonym: symplesiomorphy
comment: This term is usually contrasted to apomorphy.

Axiom
annotated source: in plesiomorphy relationship with
annotated property: IAO_0000115
annotated target: Historical homology that is based on distant shared ancestry.
has db xref: HOM_0000043
has db xref: ISBN:978-0252068140

in deep homology relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
sub property of: in parallelism relationship with
type: SymmetricProperty
IAO_0000115: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: deep genetic homology
has exact synonym: deep homologous to
has related synonym: generative homology
has related synonym: homoiology
comment: Used for structures in distantly related taxa.

Axiom
annotated source: in deep homology relationship with
annotated property: IAO_0000115
annotated target: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: nature07891
has db xref: HOM_0000044

in hemiplasy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: hemiplasous to

Axiom
annotated source: in hemiplasy relationship with
annotated property: IAO_0000115
annotated target: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
has db xref: pnas.0807433105
has db xref: HOM_0000045

in gametology relationship with
type: ObjectProperty
sub property of: in chromosomal homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: gametologous to

Axiom
annotated source: in gametology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
has db xref: HOM_0000046
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/11110898

in chromosomal homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: MeSH:Chromosome_Pairing
has exact synonym: chromosomal homologous to

Axiom
annotated source: in chromosomal homology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
has db xref: HOM_0000047
has db xref: ISBN:0195307615

in many to many orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in many to many homology relationship with
type: SymmetricProperty
IAO_0000115: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: many to many orthologous to
has exact synonym: many-to-many orthology
has exact synonym: many:many orthology
has exact synonym: trans-orthology
has related synonym: co-orthology
has related synonym: trans-homology

Axiom
annotated source: in many to many orthology relationship with
annotated property: IAO_0000115
annotated target: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
has db xref: 415741a
has db xref: HOM_0000048
has db xref: homology method.html

in within-species paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
property disjoint with: in between-species paralogy relationship with
IAO_0000115: Paralogy that involves genes from the same species.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: within-species paralogous to

Axiom
annotated source: in within-species paralogy relationship with
annotated property: IAO_0000115
annotated target: Paralogy that involves genes from the same species.
has db xref: HOM_0000049
has db xref: homology method.html

in between-species paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
IAO_0000115: Paralogy that involves genes from different species.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: between-species paralogous to
comment: The genes have diverged before a speciation event.

Axiom
annotated source: in between-species paralogy relationship with
annotated property: IAO_0000115
annotated target: Paralogy that involves genes from different species.
has db xref: HOM_0000050
has db xref: homology method.html

in postdisplacement relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
IAO_0000115: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: post-displacement

Axiom
annotated source: in postdisplacement relationship with
annotated property: IAO_0000115
annotated target: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
has db xref: Pedomorphosis
has db xref: HOM_0000051

in hypermorphosis relationship with
type: ObjectProperty
sub property of: in peramorphosis relationship with
type: SymmetricProperty
IAO_0000115: Peramorphosis that is produced by a delay in the offset of development.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in hypermorphosis relationship with
annotated property: IAO_0000115
annotated target: Peramorphosis that is produced by a delay in the offset of development.
has db xref: Peramorphosis
has db xref: HOM_0000052
has db xref: ISBN:978-0674639416

in synology relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
IAO_0000115: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: synologous to

Axiom
annotated source: in synology relationship with
annotated property: IAO_0000115
annotated target: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
has db xref: http://dx.doi.org/10.1007/BF00173425
has db xref: S0168-9525(00)02005-9
has db xref: HOM_0000053

in isoorthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in equivalogy relationship with
type: SymmetricProperty
IAO_0000115: Orthology that involves functional equivalent genes with retention of the ancestral function.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has db xref: ECO:0000080
has exact synonym: isoorthologous to

Axiom
annotated source: in isoorthology relationship with
annotated property: IAO_0000115
annotated target: Orthology that involves functional equivalent genes with retention of the ancestral function.
has db xref: S0168-9525(00)02005-9
has db xref: HOM_0000054

in tandem paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
IAO_0000115: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: tandem paralogous to
has related synonym: iterative paralogy
has related synonym: serial paralogy

Axiom
annotated source: in tandem paralogy relationship with
annotated property: IAO_0000115
annotated target: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
has db xref: S0168-9525(00)02005-9
has db xref: HOM_0000055
has db xref: ISBN:978-0878932665

in latent homology relationship with
type: ObjectProperty
sub property of: in parallelism relationship with
sub property of: in syngeny relationship with
type: SymmetricProperty
IAO_0000115: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: apomorphic tendency
has exact synonym: cryptic homology
has exact synonym: latent homologous to
has exact synonym: underlying synapomorphy
has related synonym: homoiology
has related synonym: homoplastic tendency
has related synonym: re-awakening
comment: Used for structures in closely related taxa.

Axiom
annotated source: in latent homology relationship with
annotated property: IAO_0000115
annotated target: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: j.jhevol.2006.11.010
has db xref: http://dx.doi.org/10.1186/1742-9994-2-15
has db xref: HOM_0000057
has db xref: ISBN:0199141118

in syngeny relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
type: SymmetricProperty
IAO_0000115: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: generative homology
has exact synonym: syngenous to
comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.

Axiom
annotated source: in syngeny relationship with
annotated property: IAO_0000115
annotated target: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
has db xref: http://dx.doi.org/10.1186/1742-9994-2-15
has db xref: HOM_0000058
has db xref: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R

in apparent orthology relationship with
type: ObjectProperty
sub property of: in 1 to 1 homology relationship with
sub property of: in between-species paralogy relationship with
type: SymmetricProperty
IAO_0000115: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: 1:1 paralogy
has exact synonym: apparent 1:1 orthology
has exact synonym: apparent orthologous to
has exact synonym: pseudoorthology
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.

Axiom
annotated source: in apparent orthology relationship with
annotated property: IAO_0000115
annotated target: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000060
has db xref: homology method.html

in pseudoparalogy relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
IAO_0000115: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: pseudoparalogous to
comment: These genes may come out as paralogs in a single-genome analysis.

Axiom
annotated source: in pseudoparalogy relationship with
annotated property: IAO_0000115
annotated target: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000061

in equivalogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
sub property of: in functional equivalence relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves functional equivalent genes with retention of the ancestral function.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: equivalogous to
comment: This may include examples of orthology, paralogy and xenology.

Axiom
annotated source: in equivalogy relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves functional equivalent genes with retention of the ancestral function.
has db xref: gkl1043
has db xref: HOM_0000062

in interology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: interologous to

Axiom
annotated source: in interology relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
has db xref: gr.1774904
has db xref: science.287.5450.116
has db xref: HOM_0000063

in functional equivalence relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
IAO_0000115: Similarity that is characterized by interchangeability in function.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has related synonym: functional similarity

Axiom
annotated source: in functional equivalence relationship with
annotated property: IAO_0000115
annotated target: Similarity that is characterized by interchangeability in function.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: 415741a
has db xref: HOM_0000065

in iterative homology relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
IAO_0000115: Biological homology that involves parts of the same organism.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: iterative homologous to

Axiom
annotated source: in iterative homology relationship with
annotated property: IAO_0000115
annotated target: Biological homology that involves parts of the same organism.
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000066

in paraxenology relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
IAO_0000115: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: duplicate xenology
has exact synonym: multiple xenology
has exact synonym: paraxenologous to

Axiom
annotated source: in paraxenology relationship with
annotated property: IAO_0000115
annotated target: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
has db xref: HOM_0000068
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in plerology relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
IAO_0000115: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: plerologous to
comment: This phenomenon is usually due to gene conversion process.

Axiom
annotated source: in plerology relationship with
annotated property: IAO_0000115
annotated target: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
has db xref: HOM_0000069
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in homotopy relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
property disjoint with: in homeosis relationship with
IAO_0000115: Structural homology that involves structures with the same or similar relative positions.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: homotopous to
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.

Axiom
annotated source: in homotopy relationship with
annotated property: IAO_0000115
annotated target: Structural homology that involves structures with the same or similar relative positions.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: HOM_0000071
has db xref: ISBN:0123195837

in homeosis relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
IAO_0000115: Biological homology that involves an ectopic structure and the normally positioned structure.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has related synonym: heterotopy

Axiom
annotated source: in homeosis relationship with
annotated property: IAO_0000115
annotated target: Biological homology that involves an ectopic structure and the normally positioned structure.
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: j.cell.2008.06.030
has db xref: HOM_0000072

in homoeology relationship with
type: ObjectProperty
sub property of: in ohnology relationship with
sub property of: in synology relationship with
type: SymmetricProperty
IAO_0000115: Synology that results from allopolyploidy.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: homoeologous to
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.

Axiom
annotated source: in homoeology relationship with
annotated property: IAO_0000115
annotated target: Synology that results from allopolyploidy.
has db xref: pnas.0505156102
has db xref: HOM_0000073

in paramorphism relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
sub property of: in iterative homology relationship with
type: SymmetricProperty
IAO_0000115: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has related synonym: axis paramorphism

Axiom
annotated source: in paramorphism relationship with
annotated property: IAO_0000115
annotated target: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
has db xref: s10441-007-9023-8
has db xref: j.1525-142x.2000.00054.x
has db xref: HOM_0000074

in regulogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
IAO_0000115: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
creator: Q54985720
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has exact synonym: regulogous to

Axiom
annotated source: in regulogy relationship with
annotated property: IAO_0000115
annotated target: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
has db xref: gr.1774904
has db xref: HOM_0000075

has increased age-specific mortality rate
type: DatatypeProperty
range: Datatype
  on datatype: short
  with restrictions:
    min inclusive: 0
  with restrictions:
    max inclusive: 100
IAO_0000115: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2018-05-22T16:43:28Z
comment: This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.

Axiom
annotated source: has increased age-specific mortality rate
annotated property: IAO_0000115
annotated target: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
has db xref: PMID:24138933
has db xref: Wikipedia:Infant_mortality

CL_0000540
type: Class
equivalent class: Restriction
  on property: is neuron
  has self: true

GO_0004842
type: Class
subclass of: Restriction
  on property: is ubiquitination
  has self: true

GO_0016301
type: Class
subclass of: Restriction
  on property: is kinase activity
  has self: true

GO_0019107
type: Class
subclass of: Restriction
  on property: is myristoyltransferase activity
  has self: true

obsolete exposure event or process
type: Class
IAO_0000112: An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
IAO_0000112: An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
IAO_0000115: OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
IAO_0000116: This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
creator: https://orcid.org/0000-0002-6601-2165
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-06-05T17:55:39Z
deprecated: true

sequentially ordered entity
type: Class
subclass of: Restriction
  on property: has subsequence
  some values from: sequence atomic unit
IAO_0000115: Any entity that is ordered in discrete units along a linear axis.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

sequence atomic unit
type: Class
subclass of: sequentially ordered entity
IAO_0000115: Any individual unit of a collection of like units arranged in a linear order
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.

sequence bearer
type: Class
subclass of: sequentially ordered entity
IAO_0000115: Any entity that can be divided into parts such that each part is an atomical unit of a sequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.

system
type: Class
subclass of: BFO_0000040
IAO_0000115: A material entity consisting of multiple components that are causally integrated.
IAO_0000116: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.jbiomedsem.com/content/4/1/43

UBERON_0001062
type: Class
equivalent class: Restriction
  on property: is anatomical entity
  has self: true

axiom holds for all times
type: NamedIndividual
IAO_0000115: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

relation has no temporal argument
type: NamedIndividual
IAO_0000115: ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)